I have downloaded hijack this but it wont let me make a log because my adobe acrobat wont read a file that doesn't start with %pdf.
Where does acrobat come into the equation?

You can open the hijackthis.log with notepad or any text editor. However when you save the scan to your HDD, hijackthis automatically opens the .log file, usually with notepad.

Is it possible that you have accidently set .log files to be opened by acrobat reader?