I will have a vacation in Thailand and Myanmar for three weeks in August/September: One week Thailand, a couple of days Myanmar, then back to Thailand.

Before the recent crackdown on in-and-out and overstayers the 30-days exemption would just have worked fine for such trip, but now I'm worried that I could be refused entry when coming back from Myanmar.

Do you think I should get a multiple entry tourist visa? Or would I not be affected by the new regulations because I'm not hopping in-and-out but will in fact spend some time in Myanmar?

No - you will be fine. Just make sure you have a copy of your onward flight if asked, otherwise, don't worry about it.

The recent and up coming changes are not meant to effect tourists. You can still do your trip as planned.

If you haven't planned to already, do make sure you get a tourist visa in advance of your trip to Myanmar from the embassy in Bangkok, info can be found in the Myanmar Visa section

Also note the closed days for the Myanmar Embassy in Bangkok here

Despite what may be seen around the web, there is no "Visa On Arrival" for tourists arriving to Myanmar yet (this is different to a pre-arranged visa which can be obtained in some circumstances)

Enjoy your trip.