Volk...I don't know how much help I can be but here's a couple of thoughts assuming you have the link2000r instructtion manual on board with you (as distinct from the link2000 other manual).
1. First...are you SURE you are getting high voltage to your batteries? Check using a separate voltmeter at the terminals of one of your batteries while the engine is running with the alternator on. You should see a MAXIMUM of 14.6 volts...anything over that indicates a problem.
2. Assuming there is a problem...then you should follow the "over voltage" troubleshooting steps found on the far right of page 18 of your manual:
A: With Engine off make sure the GREEN LED Reg On lite is not lit. If lit ...reverse shunt sense leads (see wiring diagram) If not...
B:Is the RED LED on the ideal charge OUTPUT MODULE LIT? (Should not be) If it is...disconnect the brown REG ON wire. If lite stays lit you have a bad output control module (regulator!). If lite goes out the problem is IN the Alternator or the alternator wiring. If lite was out to begin with...
C: Do Progress Check #1 steps found on page 11 of the manual.
I am assuming that the link 2000r was installed correctly and working before this and this is a new problem. The above steps will at least let you know whether you need to contact Xantrex...have a bad wire....or have a bad alternator.
If you do NOT have a copy of the link2000r part of the manual...you can download it here:
Good luck with it!
.see the manual link above if you think you can be of more help...the 2000r includes an external regulator/shunt and standard link2000 panel. Last couple of pages of the manual show the entire wiring layout.