First off, howdy, welcome to the Forum. Glad you're enjoying your Omicron.
To your question, the general rule for rate is 'charge in one or two hours' if possible. So either is OK, if you're doing IMR batteries I'd go with 650mA as long as it didn't get too hot.
Don't discount the idea your battery could be at end of life, this is really tough duty for these little guys, we beat 'em up a lot.
As to making better contact with batteries, I find with mine if I rotate the battery in the charger when the light doesn't come on, that generally fixes it. Also pushing them down some against the spring and letting the spring carry it up (gently) helps as well.
Also, if you like the stock 14650s you'll absolutely love IMR 14500s, lower capacity (600mAh) but something like a 20% boost in initial power and it stays hot longer. To do it you'll need the upgrade kit (comes with short tube and the needed battery) or the longer tail cap from the HV upgrade kit (or some other 15 mm spacer).
Good luck.
OF
Thanks for the quick response, however the red charge light did not turn on when I had the setting at 650. Also, sometimes I leave my batteries on my charger overnight for over eight hours, does that damage my batteries? How long do they usually last if I frequently use it everyday?
And I have been reading all the great reviews on the 14500S and I was really tempted to order them when I ordered the new charger, but I just purchased a bunch of the 14650S and I didn't want them to go to waste. Do they hold a charge longer using the 1.5s or is it just the boost in power?