On my system, using foobar2000's convert function for a full album is much slower than indivudally running each track one at a time using some other conversion tool. The cause for this is simply that my system converts fast enough on a single thread that the multi-threading is simply causing my Hard disk's buffer to fill and have to split its attention between the multiple threads trying to write their data. This is amplified on FLAC->WAV conversions where there are very large files being handled.

Anyway, I looked through the options in foobar2000, but I'm not seeing any way to disable this "multi-threading" feature for format conversions. Can anyone point me in the right direction to fix this?
Thanks

Preferences > Advanced > Tools > Converter > Thread count

I don't have that... Just Threading Priority. Is that 0.9.5 only?

Thread count should be just above threading priority. What version are you using?