SourceTree Won't Show All My Changes

Change The Maximum Lines And Size In Options

Tools > Options > Diff

Change Max Diff Line Count And Change Size Limit (Text)

I'm adding this answer as another possible cause of SourceTree "only showing the change history for a single file". This was annoying me for quite a while. No settings changes would display more than one file. THEN, I realised that the commit summary is actually a panel which slides up over the file list. ZOMG.

Make sure your filter is setup correctly:

For me the filter bugged out and while the main text said "Pending files", the dropdown had nothing selected.