I came in 2 days ago after my 4th entry this year including one border hop about 4 months ago without any hassles at all.

I come in and out of Thailand on two different passports reasonably frequently and it's no problem but as far as they are concerned it is like only having one when it comes to visas. The Immigration officer is more concerned with where you are coming from so I find it is better to use the one with some kind of record of your last exit port otherwise they think you're trying to hide something.