I experience this everyday. I notice that Solidworks loves to rebuild, sometimes for nothing at all. If this is an assembly, sometimes one component deep inside the assembly may want to be rebuilt for whatever reason, causing Soliworks to want to resave the rebuilt version of this file. It can be a pain to find out which part is causing the rebuilt flag, but what I started doing (if you use Solidworks PDM) I look at my PDM add-in window and look for a "Pencil". This is a flag for a file that has been edited but not saved. Usually opening up and saving this file and treeing all the way back up to my main assembly will fix this flag. Hope this helps. Here is a screen shot of the PDM add-in and symbol list.