3sp auto W/od stuck in 2nd

I have a 95 Eclipse GS with a 3 speed automatic transmission with overdrive that intermittently gets stuck in 2nd gear (safe mode?). Took it to a local transmission shop and was told that the code said that engine was out of time and because engine was running poorly it MIGHT be causing the transmission to go to safe or fail safe mode. I had a new timing belt put on and engine is in time now, but it happened again last night. If I let car set for a while, it will shift OK. Seems to happen on the down shift from third to second when slowing. Any suggestions or recommendations.

3 speed auto...? Since when did they ever put one of those in a 2g?

There should be a vacume line that runs into the transmission, I'm not sure where it is but I know most auto trannys have it. It lets the transmission know when to shift by reading vacum pressure from the motor. Check to see if yours is hooked up properly (look in a chiltons manual for location). If that doesnt fix it your best bet will be to take it to the tranny shop.