The way my installer put in the manifold, it was upside down.  As a result, the little glass GPM indicators don't work, since they point down.  However, now that the unit has been running for 8 months maybe, I've noticed that there  is a little brown sediment starting to build up inside the glass indicators.  The system was flushed at the time of install.  Is this something I should worry about?  Should I try and post a picture?

I would not be happy if my car guy installed my tires upside down????? Seriously is the installer going to address that issue? The sediment could be an issue or not, hard to say. Best thing would be to monitor accumilation untill installer comes back to turn gpm right side up. At that time you could feel the sediment and make a determination based on grain size and or added or no increase in the amount.
When diong a geo install, dirt happens. Sometimes a re-purge and flush is needed, prudent. Did the installer have a screen installed on flush purge apparatus? This is not done on even commercial units, they rely on gravity and volume of container to serve as settling device for debris. On residential projects we filter down to .016.
hope this helps

Nope. He patiently explained to me that the manifold is designed for loops coming up from the bottom. In my case the loops come up on one side of the basement, run across the ceiling, and then down to the manifold....hence, installing the manifold upside down rather then making every loop pipe do a 180. He said he's complained to Rehau that the gpm indicators don't work in this kind of configuration. I wasn't worried except I can't ever tell the gpm flow of the system, and now I've seen dirt. LOL, also, the manifold has these red "caps" on it that you can screw to shut off individual loops - 4 red caps. Because the manifold was upside down during winter, condensation built up on the manifold, trickled into the caps, froze (the outgoing pipe was really cold), and blew all 4 caps off the manifold, damaging the plastic threads.

Being a common sense kind of guy, why would you purchase a manifold with diagnostic features, and then install it in a configuration that made them un-useable?  You could have built your own on-site that worked.  Just my .02  Bringing pipes around in a 180 in a parrallel path to make a connection is not the end of the world.  Good luck and keep us posted on your sediment issue.
Eric

Agree with WP. If the 180s are done in a broad sweep then they should impose minimal additional head loss.

I'd be highly annoyed at having paid for instrumentation rendered unusable by characteristics of the installation.

When I am highly annoyed with products or services as a rule I don't pay for them...

I've never provided GPM flow monitors to a closed loop customer, nor have I ever brought a manifold inside.
Silly; yes, but if you don't need it and system works wel....no harm no foul.
RE sediment; likely no cause for concern.
Keep us posted.
Joe