Over here I'm mixing old and new power supplies and generally I don't see any difference on function or quality as long as the supplies match the spec regarding volt and of course ampere. Perhaps you have "dirty" power that makes cheap switching PSUs unbehave?
Yeah, I had a feeling it was one of the new third-party supplies. The ones I've seen are light and flimsy and feel as if they're made out of paper. Newer supplies of higher quality should work as well as the originals; the challenge is to find them. Glad the genuine Atari supply fixed the problem.