Random rows being overwritten on 'data store' workbook after copying from input workbook

Also, you don't really need to activate sheets and select ranges to be able to manipulate them. This often just slows things down.
The two lines below should do the same as your 5 lines above.

Windows("Main.xls").Range("B4").Copy
Windows("DataStore.xls").Range("E" & Rows.Count).End(xlUp).Offset(1).PasteSpecial Paste:=xlPasteValues

BSB