Try to preserve the old position properly during the migration to the new system.

Bar.lua

@@ -220,6 +220,10 @@ function Bar:UpgradeConfig()
 			pos.relPoint = nil
 		end
 	end
+	if version < 3 then
+		-- Size adjustment is done in first SetSize
+		self.needSizeFix = true
+	end
 	self.config.version = Bartender4.CONFIG_VERSION
 end
 
@@ -256,6 +260,16 @@ end
 function Bar:SetSize(width, height)
 	self.overlay:SetWidth(width)
 	self.overlay:SetHeight(height or width)
+	if self.needSizeFix then
+		self:SetWidth(width)
+		self:SetHeight(height or width)
+		local x, y = self:GetLeft(), self:GetTop()
+		self:ClearSetPoint("TOPLEFT", UIParent, "BOTTOMLEFT", x, y)
+		self:SetWidth(1)
+		self:SetHeight(1)
+		self:SavePosition()
+		self.needSizeFix = nil
+	end
 end
 
 function Bar:GetConfigAlpha()

Bartender4.lua

@@ -20,7 +20,7 @@ local defaults = {
 	}
 }
 
-Bartender4.CONFIG_VERSION = 2
+Bartender4.CONFIG_VERSION = 3
 
 function Bartender4:OnInitialize()
 	self.db = LibStub("AceDB-3.0"):New("Bartender4DB", defaults)

ButtonBar.lua

@@ -155,8 +155,8 @@ function ButtonBar:UpdateButtonLayout()
 
 	self:SetSize((self.button_width + hpad) * ButtonPerRow - pad + 8, (self.button_height + vpad) * Rows - pad + 8)
 
-	local anchor = self:GetAnchor()
 	-- anchor button 1
+	local anchor = self:GetAnchor()
 	buttons[1]:ClearSetPoint(anchor, self, anchor, 5 - (self.hpad_offset or 0), -3 - (self.vpad_offset or 0))
 
 	local h1 = (self.config.position.growHorizontal == "RIGHT") and "LEFT" or "RIGHT"