Here's more info for you on the subject...
 
Verify that the oscillator can on the
KREF3 is fully plugged in and is not in
backwards. (Make sure you didn't cut the pins too short!)
 
Make sure all internal cables
are plugged in, specifically the cables
between the KREF3 and KSYN3 modules
(synthesizers). As you said they were...
 
Try removing the 2nd
synthesizer (for the sub receiver), and set
CONFIG:KRX3 to NOT INST. If this
eliminates the error, the sub synth may be
defective. 
You can also try swapping it
with the main synth to see if it can be
calibrated in this slot.  That one solves a LOT of problems.
You should be able to move the cables over to the Sub board if you have it.

 
> Date: Fri, 6 Aug 2010 14:02:48 -0700
> From: ae...@worldwidedx.com
> To: elecraft@mailman.qth.net
> Subject: [Elecraft] K3 error during synthesizer calibration
> 
> All,
> 
> I just finished up the majority of the build and am attempting to do the
> Synthesizer calibration. It goes through the process and reports ERR VCO
> 00005. I've inspected the cables between the KREF and KSYN3 and also the
> TCXO installation as suggested by the manual. I can't find anything wrong.
> 
> The other weird thing is that the unit will never completely power down.
> When you try to power off, the display clears but stays lit. If you unplug
> the power and plug it back in, the display lights up with no information
> displayed. I don't believe that it 't started doing this until I tried to
> calibrate it.
> 
> I've got a call in to tech support but while I'm waiting for a call back,
> any ideas?
> 
> Tim
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