The initial timer value you set to 600017 might be off by one, because:
1 2 3 4 5 6 7
| $ bc bc 1.06.95 Copyright 1991-1994, 1997, 1998, 2000, 2004, 2006 Free Software Foundation, Inc. This is free software with ABSOLUTELY NO WARRANTY. For details type `warranty'. 8192*2/3 5461 |
bc? You heathen! dc is the One True Calculator!

It's possible that I set the value off by one, but I don't think it's likely. I set the timer value to the maximum, 255, so the interrupt should fire every other time the timer increments, ie, 16384/2 = 8192. It does so in TiEmu.
I think OSC2 (the base oscillator for int1, int3, and int5) is just running slow because my real-time clock (which is incremented in int3) is running slow, at about 72% of real time. I estimate it's 72% (my previous estimate was 67%) because I left Punix running for almost 9 hours today at work, but only 6.5 hours elapsed in Punix-land. Int1 and int3 are synchronized with each other (int1 running at 1/256 the rate of int3), so int5 must be synchronized too. I think I can live with the slow clock since I am already planning to add support for adjusting the real-time clock frequency (ie, by adding slightly more than 1 second each int3).
There's also a little issue with the screen not shutting off when I turn off the calculator, but that should be easily fixable.
The screen status bit is 60001D:4 on HW1 (on HW2, it's a bit for the contrast...), 70001D:1 on HW2.
I'll look into my poweroff routine to make sure I'm setting/clearing the right bits.
Very nice progress!
Really makes me want to install this on my 92+

Also, is the top that is running a direct port, or did you modify/make your own?
Thanks! It's not ready to use for real yet (for one, there's no filesystem in this version).
I wrote my own top program. It's really simple, though: it doesn't attempt to minimize writes to the screen by printing only differences between updates (as some versions appear to do), and it doesn't put the terminal into non-canonical input mode (so you have to type ENTER or ctrl-D before top will read user input). Also, different *nix systems have different ways to access information about the system and about individual processes, and I chose to follow the FreeBSD conventions here (ie, using the sysctl syscall).
DJ_O: It should run on the TI-89 (but not the Titanium) since the hardware is almost identical to the TI-92+, and it works just as well in TiEmu. If anyone wants to donate a TI-89 to me for testing, I'll gladly accept it.

Otherwise I'll just have to buy one myself.