I have the same Clie and also use that hack. I am having no problems with the icons, and just tried to replicate your problem. I didn't have a problem with 3.35 or any previous version either....
It sounds like you're assuming the hack is the problem. Have you actually disabled it to make sure? (I did, and you're totally right -- it looks so much better with v3b...but then everything does!
)
Another idea might be to wipe iSilo out with something like Uninstall Hack and then reinstall the beta.