There should be little white marks on either side of each robot joint indicating the zero position. You can set the zero reference position by jogging the robot until the marks on all the joints are lined up, and then selecting the "zero position master" option from the MENU->SYSTEM->MASTER/CAL menu. After you've done that, select CALIBRATE from the same menu. Does that answer your question?
Hmm. Well, one option might be to restore the controller's factory default settings by performing an INIT START. This would overwrite all programs and settings currently on the controller so you should make a backup of anything you want to keep. I was having trouble mastering an LR Mate 200iC with an R-30iA controller a few weeks ago, and restoring factory defaults fixed the problem.
You can do this by turning the controller off and holding the F1 and F5 keys on the teach pendant while turning the controller back on. This should bring up the boot monitor menu (if it doesn't, try holding PREV and NEXT instead of F1 and F5). From this menu you can select the INIT START option. Once that's finished, press the FCTN key and select the "start (cold)" option. The controller should now be back to factory defaults.
Fanuc does not set the quick master by default for some reason. The robot ships with a teachpendent box that contains the teach pendent and a bag of fuses. also included is a sheet of paper with the encoder counts. it will list them by axis. $DMR_GRP[1].Master_Coun[1]
if you go into your reference counts and put these values in, and zero out all of the ref positions (they are in radians) set the quick_master variable to TRUE, and you should be able to move back to zero, and quick master. this will restore your factory counts.
example
lets say that your sheet has these numbers on it. currently your actual numbers dont match, but we will make them.
$DMR_GRP[1].$Master_Coun
[1] 45657
[2] 987654
[3] 48465
[4] 9987622
[5] 1111
[6] 12377
[7] 0
[8] 0
[9] 0
set your ref counts equal to the above numbers.
$DMR_GRP[1].$Ref_Count
[1] 45657
[2] 987654
[3] 48465
[4] 9987622
[5] 1111
[6] 12377
[7] 0
[8] 0
[9] 0
Set the reference position to exactly zero. if you use the set quick reference it will often put the angle at something like -.00 so go in and turn them all to 0.00
$DMR_GRP[1].$Ref_Pos
[1] 0.000
[2] 0.000
[3] 0.000
[4] 0.000
[5] 0.000
[6] 0.000
[7] 0.000
[8] 0.000
[9] 0.000
set the quick master set to true so that you can use it to restore mastery.
$DMR_GRP[1].$REF_DONE = TRUE
then go back to your mastery screen and choose quick master, then calibrate.
run it to zero, if you are off it will be by a single motor revolution. overshoot the witness mark and try it again. eventually they will all snap into position. if your new mastery counts don't match up at all, bu the position is correct it probably just lost the motor revolution info. the new counts will be off by a factor of exactly 2^18 . as there are 524288 counts in a single motor revolution. the high order bits are where the motor revolutions are saved, and there is no good way of getting that back.
hope this helps. good luck
Hi DuhbCakes, thanks for the reply, could you please explain what does happen when a quick master is performed?
I thought that when the mastering is done on the zero position, it just copies the ref count values into the master count values and adjust the actual pulse counts repairing some small error that might have happened when the position was manually set.
As for the sheet, the problem is that I wasn`t in the company when the robot got installed and it seems that this data sheet was lost. 
FYI, for those with no Master sheet. You can request this from Fanuc, using the robot F number. At least I have, as associated integrator.
