Double check to make sure you have the strobes set properly to TTL or Manual (the TTL switch on the DS-50 needs to have the bottom part over the TTL lettering) and that you have set up the housing, strobe and cords properly in accordance with the Ikelite manuals.
Now that part is out of the way, and to give you a heads up just in case, when I started seeing what is happening to you I first noticed that my camera was not reacting (releasing shutter) properly underwater and the strobes seemed to be firing/not firing like you described, but thought I was imagining it. (Note this was not a Canon XTi setup though)
Anyway, I then noticed on a subsequent dive that there was some water in the bottom of the housing, kept it level and camera was okay, but for a little salt on the bottom.
Checked everything back at the hotel and made sure everything was okay, and had three other people also check it. Housing was fine and dry at depth and I figured I must have messed up before.
So anyway, at depth I pressed the shutter release and tried to take the first shot. Again there seemed to be delays and strobe misfires. Tried a few more times with different settings to see if the strobes would work (one off and one on worked) then after taking many shots of myself to look at the strobes, I gave up and went with just one strobe. Then I noticed again that there was water in the bottom of the housing.
Returned the housing to Ikelite and they found no problem - it pressure tested fine, everything was okay and they returned the housing to me. But I remained uncomfortable and returned the housing one more time (had not used it since it was returned the first time) prior to leaving on a trip for two weeks. This time they found a leak in the shutter release gland, which is why the leaks would not start until I started shooting, and replaced them all.
Took the camera on the two week trip, and the DS-125 would not fire at all. Tried for a couple of hours to get it firing (I bring a few cords with me and the DS-50 fired fine), gave up and shot two dives with the DS-50 (and the housing did not flood) then shot video the rest of the way.
Anyway turns out this time was a defective flash tube in the DS-125 and they repaired it.
So for me, the issue may have been the leak and/or something amiss in the DS-125 itself.