Hi David,
on your '97 SL, the flip key performs two different main functions.
1. It provides access authorization when you press the button.
2. It provides drive authorization when you insert it into the ignition lock.
The second function is totally independent from the first. Even if batteries are removed from the key, the chip in the key is recognized through the black plastic ring on your steering lock as a valid transponder and the car should start even if you didn't unlock it with the remote.
Therefore is a key that doesn't start the car faulty and needs renewal unless it's key-track was disabled by the dealer for anti-theft purpose.
Get 2 new keys. Nothing you can do otherwise.
The window problem is not related. It's a microswitch in the door lock that usually causes this fault. You can adjust it! Check it out.
All the best,
Dokta