I have: http://windows.github.com/
My current project has around 20k files, around 150MB (and not speaking about how slow it is and I cannot do a thing now) it doesn\'t
I had an interesting issue - even though I had an excel file open called "Combined - ForImportv4.xlsm", Git UI had no problem checking that in but it gave the error in the OP's subject for the backup file "~$Combined - ForImportv4.xlsm" so I discarded that change and all went through.
PS: As for why i'm checking an Excel file into Git ... just don't got there :)...