This sounds like S2 sleep mode. It's possible that with the loss of cmos settings, your motherboard changed the type of sleep it goes into.
First, go to power options. If the power button is configured to put the computer to sleep, then this is most certainly the problem.
Enter your motherboard settings by rebooting and pressing the corresponding button the startup screen says will bring you to settings. It might be delete, F1, F2, F12...
Next, look through all the power related settings for something that says S1 or S2. Set it to S3.
Save the settings (they won't save if you don't have a good battery in the motherboard). Enjoy.