Following up for anyone else who may have the problem. Had a discussion with the local Kubota dealer. It apparently happened because the FEL and was engaged while the scraper (3point hitch) was in detent, causing the two to fight against each other. I'm no mechanic, but that makes sense to me. It only happened when both were engaged at the same time.
First, see if you can duplicate the occurrence. That would verify what the dealer told you and your tractor problems are over for now.
The dealer is basically saying that it is "operator error". This is a common excuse for when a dealer somehow screws up and wants to cover his/her behind.
However, it is my experience that if the FEL and the 3PH are "fighting against each other" then one of the two functions will not work or will tend to be jerky.
Once again, the engine in the BX is not going to die because of the hydraulic pump being balky.
Try crawling under the tractor with a flashlight and check the filter that is there. It is opaque plastic so the element should be clean if it was recently changed. If the element is dark then something is amiss.
Here is what it looks like:
http://www.messicks.com/partdetail/12581-43012.aspx
EDIT: Ooo...this is kind of special a 360° view:
http://www.messicks.com/360parts/viewer.aspx?make=KU&part=12581-43012
The filter could have not been changed or the fuel is contaminated and dirty.
I hate to be negative but the dealer's explanation just doesn't add up. I've operated my BX often in those circumstances (rear in relief and FEL in use) and it has never coughed or died.