Moved all calls to StaticPopupHide() from addon:CloseWindow() (and all other places they were used) to addon:ClosePopups() since this is used in quite a few places, some without hiding the main frame. Added ARL_SEARCHFILTERED to ClosePopups(), as it was used in two other places but missing here.

diff --git a/ARLFrame.lua b/ARLFrame.lua
index 362cc6a..3aa5ca5 100644
--- a/ARLFrame.lua
+++ b/ARLFrame.lua
@@ -24,37 +24,30 @@ local L			= LibStub("AceLocale-3.0"):GetLocale(MODNAME)
 local QTip		= LibStub("LibQTip-1.0")
 local QTipClick		= LibStub("LibQTipClick-1.1")

+-------------------------------------------------------------------------------
+-- Upvalued Lua globals
+-------------------------------------------------------------------------------
 local string = string
-local ipairs = ipairs
-local tinsert = tinsert
 local sformat = string.format
+local strlower = string.lower

--- local variables for this file. Must be used by multiple functions to be listed here
-local currentProfIndex = 0
-local currentProfession = ""
-local maxVisibleRecipes = 24
-local FilterValueMap = {}
-local sortedRecipeIndex = {}
-local DisplayStrings = {}
-local myFaction = ""
-
-local narrowFont = nil
-local normalFont = nil
-
-local pairs = pairs
 local select = select
 local type = type

 local table = table
 local twipe = table.wipe
 local tremove = table.remove
-local tonumber = tonumber
+local ipairs = ipairs
+local pairs = pairs
+local tinsert = tinsert

+local tonumber = tonumber
 local math = math
 local floor = math.floor

-local strlower = string.lower
-
+-------------------------------------------------------------------------------
+-- Upvalued Blizzard globals
+-------------------------------------------------------------------------------
 local GetSpellInfo = GetSpellInfo
 local GetSkillLineInfo = GetSkillLineInfo
 local GetNumSkillLines = GetNumSkillLines
@@ -64,13 +57,26 @@ local GetTradeSkillLine = GetTradeSkillLine
 local GetItemInfo = GetItemInfo
 local UnitClass = UnitClass

-
 -- Modifier functions which we deal with
 local IsModifierKeyDown = IsModifierKeyDown
 local IsShiftKeyDown = IsShiftKeyDown
 local IsAltKeyDown = IsAltKeyDown
 local IsControlKeyDown = IsControlKeyDown

+-------------------------------------------------------------------------------
+-- Local variables. Must be used by multiple functions to be listed here.
+-------------------------------------------------------------------------------
+local currentProfIndex = 0
+local currentProfession = ""
+local maxVisibleRecipes = 24
+local FilterValueMap = {}
+local sortedRecipeIndex = {}
+local DisplayStrings = {}
+local myFaction = ""
+
+local narrowFont = nil
+local normalFont = nil
+
 local seasonal = GetCategoryInfo(155)

 -- Fallback in case the user doesn't have LSM-3.0 installed
@@ -207,17 +213,24 @@ StaticPopupDialogs["ARL_SEARCHFILTERED"] = {
 	hideOnEscape = 1
 }

--- Description:
-
-function addon:CloseWindow()

-	-- Close all possible pop-up windows
+-------------------------------------------------------------------------------
+-- Close all possible pop-up windows
+-------------------------------------------------------------------------------
+function addon:ClosePopups()
 	StaticPopup_Hide("ARL_NOTSCANNED")
 	StaticPopup_Hide("ARL_ALLFILTERED")
 	StaticPopup_Hide("ARL_ALLKNOWN")
 	StaticPopup_Hide("ARL_ALLEXCLUDED")
-	addon.Frame:Hide()
+	StaticPopup_Hide("ARL_SEARCHFILTERED")
+end

+-------------------------------------------------------------------------------
+-- Hide the main recipe frame, and close all popups.
+-------------------------------------------------------------------------------
+function addon:CloseWindow()
+	self:ClosePopups()
+	self.Frame:Hide()
 end

 -- Description: Colours a skill level based on if the player can learn it.  The recipe string is coloured based on if the player has a high enough skill level or faction to learn it
@@ -1083,7 +1096,6 @@ end
 -- Description: Scrollframe update stuff

 local function RecipeList_Update()
-
 	-- Clear out the current buttons
 	for i = 1, maxVisibleRecipes do
 		addon.RecipeListButton[i]:SetText("")
@@ -1097,11 +1109,7 @@ local function RecipeList_Update()
 	FauxScrollFrame_Update(ARL_RecipeScrollFrame, entries, maxVisibleRecipes, 16)

 	-- close all popups
-	StaticPopup_Hide("ARL_NOTSCANNED")
-	StaticPopup_Hide("ARL_ALLFILTERED")
-	StaticPopup_Hide("ARL_ALLKNOWN")
-	StaticPopup_Hide("ARL_ALLEXCLUDED")
-	StaticPopup_Hide("ARL_SEARCHFILTERED")
+	addon:ClosePopups()

 	if (entries > 0) then

@@ -1943,12 +1951,7 @@ function addon:SwitchProfs(button)
 	local endLoop = 0
 	local displayProf = 0

-	-- Close all possible pop-up windows
-	StaticPopup_Hide("ARL_NOTSCANNED")
-	StaticPopup_Hide("ARL_ALLFILTERED")
-	StaticPopup_Hide("ARL_ALLKNOWN")
-	StaticPopup_Hide("ARL_ALLEXCLUDED")
-	StaticPopup_Hide("ARL_SEARCHFILTERED")
+	self:ClosePopups()

 	-- ok, so first off, if we've never done this before, there is no "current"
 	-- and a single iteration will do nicely, thank you
@@ -3429,16 +3432,8 @@ function InitializeFrame()
 	-- Stuff in the non-expanded frame (or both)
 	-------------------------------------------------------------------------------
 	local ARL_CloseXButton = CreateFrame("Button", "ARL_CloseXButton", addon.Frame, "UIPanelCloseButton")
-	ARL_CloseXButton:SetScript("OnClick",
-				   function(self)
-					   -- Close all possible pop-up windows
-					   StaticPopup_Hide("ARL_NOTSCANNED")
-					   StaticPopup_Hide("ARL_ALLFILTERED")
-					   StaticPopup_Hide("ARL_ALLKNOWN")
-					   StaticPopup_Hide("ARL_ALLEXCLUDED")
-					   StaticPopup_Hide("ARL_SEARCHFILTERED")
-					   self:GetParent():Hide()
-				   end)
+	-- Close all possible pop-up windows
+	ARL_CloseXButton:SetScript("OnClick", function(self) addon:CloseWindow() end)
 	ARL_CloseXButton:SetPoint("TOPRIGHT", addon.Frame, "TOPRIGHT", 5, -6)

 	-------------------------------------------------------------------------------
@@ -3569,16 +3564,8 @@ function InitializeFrame()
 	local ARL_CloseButton = addon:GenericCreateButton("ARL_CloseButton", addon.Frame,
 							  22, 69, "BOTTOMRIGHT", addon.Frame, "BOTTOMRIGHT", -4, 3, "GameFontNormalSmall",
 							  "GameFontHighlightSmall", L["Close"], "CENTER", L["CLOSE_DESC"], 1)
-	ARL_CloseButton:SetScript("OnClick",
-				  function(this)
-					  -- Close all possible pop-up windows
-					  StaticPopup_Hide("ARL_NOTSCANNED")
-					  StaticPopup_Hide("ARL_ALLFILTERED")
-					  StaticPopup_Hide("ARL_ALLKNOWN")
-					  StaticPopup_Hide("ARL_ALLEXCLUDED")
-					  StaticPopup_Hide("ARL_SEARCHFILTERED")
-					  this:GetParent():Hide()
-				  end)
+	-- Close all possible pop-up windows
+	ARL_CloseButton:SetScript("OnClick", function(self) addon:CloseWindow() end)

 	-------------------------------------------------------------------------------
 	-- ProgressBar for our skills
@@ -4837,7 +4824,6 @@ function addon:DisplayFrame(
 	if (not addon.Frame) then
 		InitializeFrame()
 	end
-
 	-- Set our addon frame position
 	SetFramePosition()