More cleanup. Trying to reduce the amount of loops and functions calls that are preformed during the OnUpdate as much as possible. Also trying different ways to work with the available data. Since I'm doing everything in the background now before I display the bars, it's no longer causing that weird flicking issue. Though I'm sure I could have tackled this a bit differently, I think it works rather well the way it is now.

diff --git a/XanDebuffTimers.lua b/XanDebuffTimers.lua
index 164d292..25a3e13 100644
--- a/XanDebuffTimers.lua
+++ b/XanDebuffTimers.lua
@@ -33,8 +33,9 @@ local function Debug(...)
     if debugf then debugf:AddMessage(string.join(", ", tostringall(...))) end
 end

-timers.data = {}
-timersFocus.data = {}
+--debuff arrays
+timers.debuffs = {}
+timersFocus.debuffs = {}

 ----------------------
 --      Enable      --
@@ -271,9 +272,7 @@ end
 function f:CreateDebuffTimers()

     local Frm = CreateFrame("Frame", nil, UIParent)
-
-	Frm.data = {}
-    Frm.active = false
+
     Frm:SetWidth(ICON_SIZE)
     Frm:SetHeight(ICON_SIZE)
 	Frm:SetFrameStrata("LOW")
@@ -317,8 +316,8 @@ function f:generateBars()
 	for i=1, MAX_TIMERS do
 		timers[i] = f:CreateDebuffTimers()
 		timersFocus[i] = f:CreateDebuffTimers()
-		if not timers.data[i] then timers.data[i] = {} end
-		if not timersFocus.data[i] then timersFocus.data[i] = {} end
+		if not timers.debuffs[i] then timers.debuffs[i] = {} end
+		if not timersFocus.debuffs[i] then timersFocus.debuffs[i] = {} end
 	end

 	--rearrange order
@@ -340,8 +339,6 @@ function f:generateBars()
 end

 function f:ProcessDebuffBar(data)
-	if not data.active then return end --just in case
-
 	local beforeEnd = data.endTime - GetTime()
 	-- local percentTotal = (beforeEnd / data.durationTime)
 	-- local percentFinal = ceil(percentTotal * 100)
@@ -381,30 +378,29 @@ f:SetScript("OnUpdate", function(self, elapsed)
 	local fCount = 0

 	for i=1, MAX_TIMERS do
-		if timers.data[i].active then
-			self:ProcessDebuffBar(timers.data[i])
+		if timers.debuffs[i].active then
+			self:ProcessDebuffBar(timers.debuffs[i])
 			tCount = tCount + 1
 		end
-		if timersFocus.data[i].active then
-			self:ProcessDebuffBar(timersFocus.data[i])
+		if timersFocus.debuffs[i].active then
+			self:ProcessDebuffBar(timersFocus.debuffs[i])
 			fCount = fCount + 1
 		end
 	end

 	--no need to arrange the bars if there is nothing to work with, uncessary if no target or focus
 	if tCount > 0 then
-		f:ArrangeDebuffs("target")
+		f:ShowDebuffs("target")
 	end
 	if fCount > 0 then
-		f:ArrangeDebuffs("focus")
+		f:ShowDebuffs("focus")
 	end


 end)

 function f:ProcessDebuffs(id)
-	--only process for as many timers as we are using
-	local sdTimer = timerList[id]
+	local sdTimer = timerList[id] --makes things easier to read

 	for i=1, MAX_TIMERS do
 		local name, _, icon, count, _, duration, expTime, unitCaster, _, _, spellId = UnitAura(id, i, 'PLAYER|HARMFUL')
@@ -418,63 +414,47 @@ function f:ProcessDebuffs(id)
 			local barPercent = (totalBarLength / string.len(BAR_TEXT)) * 100

 			if barPercent > 0 or beforeEnd > 0 or totalBarLength > 0 then
-				--data
-				sdTimer.data[i].id = id
-				sdTimer.data[i].spellName = name
-				sdTimer.data[i].spellId = spellId
-				sdTimer.data[i].iconTex = icon
-				sdTimer.data[i].startTime = startTime
-				sdTimer.data[i].durationTime = duration
-				sdTimer.data[i].beforeEnd = beforeEnd
-				sdTimer.data[i].endTime = expTime
-				sdTimer.data[i].totalBarLength = totalBarLength
-				sdTimer.data[i].stacks = count or 0
-				sdTimer.data[i].percent = barPercent
-				sdTimer.data[i].active = true
+				--debuffs
+				sdTimer.debuffs[i].id = id
+				sdTimer.debuffs[i].spellName = name
+				sdTimer.debuffs[i].spellId = spellId
+				sdTimer.debuffs[i].iconTex = icon
+				sdTimer.debuffs[i].startTime = startTime
+				sdTimer.debuffs[i].durationTime = duration
+				sdTimer.debuffs[i].beforeEnd = beforeEnd
+				sdTimer.debuffs[i].endTime = expTime
+				sdTimer.debuffs[i].totalBarLength = totalBarLength
+				sdTimer.debuffs[i].stacks = count or 0
+				sdTimer.debuffs[i].percent = barPercent
+				sdTimer.debuffs[i].active = true
 			end
 		else
-			sdTimer.data[i].active = false
+			sdTimer.debuffs[i].active = false
 		end
 	end

-	f:ArrangeDebuffs(id)
+	f:ShowDebuffs(id)
 end

 function f:ClearDebuffs(id)
-	local sdTimer = timerList[id]
+	local sdTimer = timerList[id] --makes things easier to read
 	local adj = 0

 	for i=1, MAX_TIMERS do
-		sdTimer.data[i].active = false
+		sdTimer.debuffs[i].active = false
 		sdTimer[i]:Hide()
 	end

 end

-local function deepcopy(orig)
-    local orig_type = type(orig)
-    local copy
-    if orig_type == 'table' then
-        copy = {}
-        for orig_key, orig_value in next, orig, nil do
-            copy[deepcopy(orig_key)] = deepcopy(orig_value)
-        end
-        setmetatable(copy, deepcopy(getmetatable(orig)))
-    else -- number, string, boolean, etc
-        copy = orig
-    end
-    return copy
-end
-
-function f:ArrangeDebuffs(id)
+function f:ShowDebuffs(id)

 	if locked then return end
 	locked = true

-	local adj = 0
 	local sdTimer
 	local tmpList = {}
-
+
 	if id == "target" then
 		sdTimer = timers
 	elseif id == "focus" then
@@ -485,8 +465,8 @@ function f:ArrangeDebuffs(id)
 	end

 	for i=1, MAX_TIMERS do
-		if sdTimer.data[i].active then
-			table.insert(tmpList, deepcopy(sdTimer.data[i]))
+		if sdTimer.debuffs[i].active then
+			table.insert(tmpList, sdTimer.debuffs[i])
 		end
 	end

@@ -515,24 +495,22 @@ function f:ArrangeDebuffs(id)

 	for i=1, MAX_TIMERS do
 		if tmpList[i] then
-			sdTimer.data[i] = tmpList[i]
-
 			--display the information
 			---------------------------------------
-			sdTimer[i].Bar:SetText( string.sub(BAR_TEXT, 1, sdTimer.data[i].totalBarLength) )
-			sdTimer[i].Bar:SetTextColor(f:getBarColor(sdTimer.data[i].durationTime, sdTimer.data[i].beforeEnd))
-			sdTimer[i].icon:SetTexture(sdTimer.data[i].iconTex)
-			if sdTimer.data[i].stacks > 0 then
-				sdTimer[i].stacktext:SetText(sdTimer.data[i].stacks)
+			sdTimer[i].Bar:SetText( string.sub(BAR_TEXT, 1, tmpList[i].totalBarLength) )
+			sdTimer[i].Bar:SetTextColor(f:getBarColor(tmpList[i].durationTime, tmpList[i].beforeEnd))
+			sdTimer[i].icon:SetTexture(tmpList[i].iconTex)
+			if tmpList[i].stacks > 0 then
+				sdTimer[i].stacktext:SetText(tmpList[i].stacks)
 			else
 				sdTimer[i].stacktext:SetText(nil)
 			end
-			sdTimer[i].timetext:SetText(f:GetTimeText(ceil(sdTimer.data[i].beforeEnd)))
+			sdTimer[i].timetext:SetText(f:GetTimeText(ceil(tmpList[i].beforeEnd)))
 			---------------------------------------

 			sdTimer[i]:Show()
 		else
-			sdTimer.data[i].active = false
+			sdTimer.debuffs[i].active = false  --just in case
 			sdTimer[i]:Hide()
 		end
     end