How were you getting the documents to the Fiery? Were you printing from Acrobat? If you are printing from Acrobat Professional then under the Advanced button in the print dialog there are are settings around colour management that will produce the effect you are describing.
A safer way is...
As you have described the problem, the issue lies at the printers end. If the channels palette in Acrobat shows 100%K then the file is correct. I would have thought that even if the file was CMYK, any half decedent pre-press operator would be able to fix it for single colour printing.
The engine always prints at 1200dpi, it is just the raster job can be either 600dpi or 1200dpi. Usually 600dpi is the better choice, your customers won't see the difference. From memory there are some differences between the T1 and Q2 in regards to handling the clear varnish, so might want to...
The patterns are actually determined by the 'Dither Pattern' setting on the engine itself (found under Additional Functions->System Settings->Device Management->Dither Patterns). The engine can have three patterns selected at one time, two you can change yourself. The two patterns are titled...
Without seeing the resulting files that they are ending up with after their convoluted process to get the file to the RIP it is hard to say, but I agree that it is more than likely end user related.
The reason I say this is that the EFI controller* has an optional 'Rich Black' setting that...