No , having
hjt in a temp folder doesnt effect the scanning but he doesn't have
hjt in a (windows) temp folder:
C:\Downloads\HijackThis.exe
And thats the most importend part of it, its handy and cleaner to make a separete folder but aslong it isnt in a temp folder
hjt can make backups of the removed entry's and then they are immediatly stored in a "safe" location.
And if he means that he thinks he has the winfixer/vundo infection then there is indeed no trace of it.