Saturn recently replaced the PCM on my 1999 SW2 with 18,000 miles. They
did it under the Federal Emissions Warranty (* years/80,000 miles) but
tried to blame it on my alarm/cut off switch. This was professionally
installed when the car was just 1 day old. When they returned the car to
me last week, the service light was flashing, and the service engine soon
and ABS were lit. The codes, as identified by my friends shop, were P1336
and 35.) When I complained, they first told me that the crankshaft sensor
needed to be replaced and there was a short in the ABS wiring. (The first
code was actually just that the crankshaft variation was not learned and
the PCM just needed to be properly programmed.) I played dumb and asked
why these codes had not shown up before. They told me that since the PCM
was not working, the systems were not reporting that there was a problem.
I knew they were lying, since other codes had been reported when I was
diagnosising the car prior to having the PCM replaced. The next day, they
said they were able to repair the crankshaft code for free, but they would
have to charge for the ABS repair.

The ABS was fine prior to their PCM change and the car being towed. The
traction control monitor light was on, so the system was working. Now,
the TC light is off.

Could they have messed something up with the ABS when changing the PCM?

yeah they probably messed up your whole braking system. could be dangerous.
one minute you have brakes next minute you dont. i would get the braking
system checked by professionals.