All you need to convert .aiff to FLAC in Windows is Foobar2000 and FLAC v1.2.0 or newer (which can be found in TLH).

Uninstall Foobar2000 and TLH, then install the latest versions of Foobar2000 and Trader's Little Helper.
http://www.foobar2000.org/
http://tlh.easytree.org/

Drag your .aiff files into Foobar2000, select all, then right click > convert > convert to > FLAC (you can adjust the level with the '...' button > save. Done! The first time you do this Foobar may ask you for the location of the flac.exe file, it's usually in C:\Program Files > Trader's Little Helper > CmdlineApps.

I just tested it. I had a 24/96 FLAC file > dragged into Foobar2000 > converted to .aiff. Then I dragged the .aiff into Foobar2000 > converted back to FLAC > saved to a different location. The FLAC fingerprints matched!