Yeah I had problems with GTK crashing. AFAIK Phex is not ppc based, it is universal binary and 64-bit which can be checked by opening system profiler & clicking on phex. Although Mountain Lion (ML) suggests it's 32-bit perhaps due to Apple Java being both 32-bit and 64-bit.
At least on ML installing Apple Java fixes both the Phex and Acqlite startup issue.

Did you install Apple Java? If that did not fix things, did you try replacing the stub file?
You could try this as suggested by GregorK a couple years ago.

I'm not using Yosemite so I cannot check it for compatibility.