Remote Start Problem: Mechanical, Like in Gear

[Lil Abner]

So, I installed a remote start on my 09 LB a while back. I finally finished a safety circuit to ensure the car is in neutral and has the e-brake on. I've tested the function, and it's worked many times before.

Today it's could outside (25-degrees). I park in a garage, so it's closer to 40-degrees. I hit the remote start button, and the car was shaking/grinding while it cranked, then started. Once started, it purred like a kitten. I'm confused. I drove the car around, parked the car (in neutral before stopping), checked that it was in neutral by wiggling the shifter left to right (habit). Pulled the e-brake, turned the car off. Hit the remote start button. Same thing!

It seems almost like the car isn't coming out of gear. But the stick is in neutral. The car starts just fine when I push the clutch in like normal. But for some reason, when the car is in neutral, and the clutch isn't depressed, it seems like a gear is hanging.

Obviously I can't take it to the dealer. Anyone have any thoughts? The car is an 09, 5-speed, with less than 35,000 miles. The transmission/gear oil is still stock. Hopefully someone can help me out with this. I KNOW this isn't normal!!