Although it may well be true that few people are aware of BitcoinBuilder, that doesn't seem to be an adequate explanation of the GoxBTC / RealBTC exchange rate there.  Unless I'm mistaken, internal transfers at Gox were only recently suspended.  I would expect that the exchange rate at BitcoinBuilder prior to those transfers was much closer to the Gox / Bitstamp price ratio. 

Until I read this, I had wondered why MtGox suspended internal transfers.  Unfortunately, the most plausible explanation seems to be that they want to prevent a whale, in this case BitcoinBuilder, from amassing too large a share of GoxBTC (or GoxUSD).  A whale might be in a better position to identify suspicious market behavior, might have more financial incentive to pursue means to put pressure on MtGox, and might be a more formidable enemy in court.

There is obviously a lot of irrational behavior surrounding the MtGox exchange right now, so perhaps there is some danger in reading too much into divergences from fair value.  At the very least, this re-emphasizes that suspension of internal transfer is a significant new red flag added to the MtGox red flag Winter collection.