Yes, I do have a ML390S which was upgraded from a ML39, so the transport was not changed, not part of the upgrade i.e. still the original ML39.
The unit I'd purched in 1996, and lo and behold it started to play up as YOU, OP described.
So what was wrong?
The LASER was on its way out, getting to 'weak' to read double layer SACD/CDs AND on its way out, also starting to touch and mark/scratch many of my CDs. BAD!
One additional thing I found out of late, after the successful laser replacement, that the small 'plastic spider centering hub' which was originally used on the motor spindle of the ML39 had gotten 'tired' too, and split in half.
Newer Philips transport versions seem to have replaced this rather fragile centering hub with either a solid plastic or Alu part.
So it is of interest to have this also addressed when a new laser unit is fitted.
Laser unit life seems to peter out after 15-20 years, so mine lasted short of 26 years...
I hope this helps, and I do hope you'll find a reasonable repair arrangement!
Mine sounds as good as new after the laser replacement and now might outlive me?!? 🙄
M. 🇿🇦