I am currently working in Thailand and have a valid work permit, stamped untill Nov 7th of this year. The question is do I still have to report to the Immigration office after 90 days from the issue of the work permit?

I have worked here before and didn't have to do this but the times they are a changin.

You must report your address 90 days after your arrival in Thailand and every 90 days thereafter. As you seem to be on an extension of stay rather than a 90 day entry you do need to report. You do not report when outside of Thailand and the clock starts again the day you arrive (fill out arrival TM.6 card).