About 4 months ago, I had to have a new windshield fitted because of an impact that cracked the original. So I took it to a local, reputable body shop for their "guy" to fit a new one. I have never been real happy with the way that the rubber seal seemed to contact the roof, just didn't seem as tight to the roof as before. Now the headliner is starting to separate on the drivers side. Is this caused by the bad seal, or just a common problem that I've seen other members comment on?

 

Headliner sagging is very common on these cars as they age. I just re-upholstered mine, it was a pain in the butt but worth it since new ones are crazy $$.
You can try re-gluing the sagging section but it's a temporary fix at best. There's a thin layer of foam between the fabric and backer board that has deteriorated. Without cleaning off the old foam and adhesive the new adhesive will have a hard time doing its job.

I very much doubt this is related to the windshield, but you might want to carefully check for water leaks just in case.
When I had the windshield on my 128i replaced last year I had the same problem with the rubber seal. The seal was folded up and kinked when it was delivered which was causing it to not lay flat against the front edge of the roof. Over time the material relaxed enough where it lays perfectly flat now.

 

I thought that it might be the foam that had deteriorated. I did one some years ago on a 1983 Golf GTI, as I recall. The biggest pain was the disassembly of everything to get the headliner thru the hatch. I'm going to do this myself, and have the new fabric as close to the Anthracite interior colour as I can get.

 

As an alternative, auto parts stores sell little clear thumbtacks with tiny cork screws. I just wanted to hold the headliner up for a week or two while I gathered the money for a new headliner job.

That was three years ago. Still looks okay. Ha!

Peter