I've been searching and I haven't quite found what I'm looking for.

I went to plug my phone into my computer to charge, and it started charging but the led blinks red and stops charging with a message "not charging". When off, it starts charging, then reboots a couple times before the led going black.

I'm hoping this is not the dreaded USB problem. It has been so good to me up to this point...

I'm new to N900 myself, but from the experience I've had with N810, I wonder if this has something to do with an aging battery. "Not charging" doesn't sound familiar but reboots do. See what /var/lib/dsme/stats/lifeguard_resets has in it -- if it lists bme_RX-51, there's a very good chance you'll have to find a new battery.

I actually do have a new battery on the way, and was thinking that could be the problem. I'll wait until it does arrive before trying anything else.

Well, out of curiosity, you could still take a look at that file. :-) My N900 doesn't have that file, but then again it hasn't had any spontaneous reboots either. However, it is present on my N810 for which I have a collection of bad batteries...

check the connectors on the battery i bent mine a bit..
The red LED appears when battery is not persent.. so might be the case..

Same problem here (since a few monthes, but never reflashed since then).
I add a few more details hoping to involve more people.
What happens is that the lower the current used to charge, the higher the percentage of charge reached BEFORE the red led
blinks and the charging process stops: i.e., charging with wall charger leads to 80% (battery charge), with usb port 70%.
After a few experiments I am now able to fully charge my mobile. I had to install i2c_tools and a slightly modified (by
me) version of joerg charging script. The modified script stop BME, loads the appropriate values on the bq 24150 charging
chip and keeps it away from being watchdog-stopped by resetting it's internal clock every 15 seconds (but doesn't read
any of the bq27200 values).
I can guess that when the problem occurs the bq27200 fails somehow, and any attempt to read it's values (battery temperature, charge percentage, etc...) leads
to a fault. In fact, with the battery fully charged if the script gets stopped and BME gets started the phone will struggle, suddenly becoming unresponsive, and I
guess that the problem is due to BME trying to read bq27200 values but not being able to.
Fortunately it looks like bq24150 keeps working properly, though ensuring a proper and hopefully safe charge.
I have to say that I had big problems with my phone, since it loose the phone signal probably after an heavy rain. It was then repaired by a third part technical
center (since Nokia refused to repair it). The battery issue strted a few weeks after the phone was repaired, so it might be related (but it might be not...).

Got the new battery yesterday and was able to charge it, so most things are good again. I do think I also have a problem with the cable going to the computer, since I couldn't charge from the computer. I'm going to replace it and see if that fixes that problem.

Thanks for the suggestions guys.