Not really issues, for basic print and/or cut it's fine... it's just such an awkward program with no features.
The set up I liked the best was Onyx that I did all the printing from for two UV printers and three Grand format R2R
and then we had three plot station that used Fine Cut and Mimaki plotters.
I could send a contour cut print 100' long and it would do perfectly because I set up the contour marks, not the
program & could have as many marks as necessary.
And as I'm sure you know, Onyx will change individual colors without changing the whole print.
Yes, one of versaworks weaknesses is that it's stuck on it's 4 circles for print/cut registration, which limits the accuracy for jobs over 4 feet long, whereas Onyx will put a mark every 18" along the print and cuts super accurate at pretty much any length. The new VG-2 machines have a feature where it will add extra crop marks on longer prints, not sure if this is done by the rip and can be achieved on other printers or if it is specific to the VG-2 machines.
Also, I do believe you can change single colours in Versaworks, but they must be spot colours, whereas Onyx will let you change CMYK or RGB colours
In the end, you get what you pay for, Versaworks works well enough for 99% of it's users, if you are constantly running up against the limits of Versaworks, an upgrade to Onyx or another full featured rip is well worth the money.