I never get to X, so not clicking on anything should be pretty easy ;)
I have modded my IA-1 a bit, but nothing that should be causing problems (I don't think). I have swapped processors for a K6-III+, changed the FSB to 100MHz, and switched the clock multiplier to 4.5x. I've also added a somewhat cranky microdrive that I use to shuttle images back and forth. (I've tried booting into Linux without the microdrive, to no avail)
As an aside, I do have a Linksys USB100TX on one of the USB controllers. The "old" midori image failed to pick it up correctly (reports it as a USB10TX instead. The "new" midori image correctly identifies it. I also had a wireless keyboard receiver plugged in, but I removed it to see if it made any difference.
I have noticed one other odd thing. Every so often, the unit won't boot Linux at all. Instead, it will just say "Loading...." and stop there. If I warm boot the system, it will usually go ahead and drop me into a prompt the next time. This doesn't occur with the MSN image, which boots just fine at 100MHz, nor does it bother Windows on the Microdrive.
The SANDisk is running at 33.3MHz, along with the rest of the PCI bus, so it shouldn't be a storage problem.