I thought I had my brakes set up pretty well on my 'cross bike, unitl this morning riding it to work and I went through a bunch of standing water and lost all braking power, front and back. Once the wheels had rotated through a few times with me holding the brakes they started to bite again and I could stop myself again, but I am concerned about racing on it now.

Brakes are Tektro wide profile with DA road pad holders, Kool Stop salmon pads in the front and black/salmon pads in the back.

Any ideas? I know this is probably a pretty vague description, so if there is any other pertinent info I am missing, please ask!

Welcome to the world of canti brakes.
They all suck when things get wet. You already have decent brakes and probably the best pads. Maybe you can dial in your setup or switch to ceramic rims or just learn to deal with it.

i would ditch the kool stop pads and run the dura ace pads, current generation (r55c3). they vastly improved their wet braking. one of the few pads that will slow you down well in a downpour. campy's stock pad compound will, too, but that would require different holders and unless they are 2011 holders, they are a pain to swap pads.
i know some people love the kool stop salmon pads, but i have always found them to be highly overrated.

Those look a lot like the Zipp Tangente Cork pads so just curious what differentiates the Shimano from the Zipp pads or is this another instance of same manufacturer, different label?

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Michael - The Anaerobic Threshold is neither...

I think you're looking at other pads. tangente cork pads are full cork, brown, and completely smooth at the rim. the r55c3 are black rubber with some shallow grooves.
it's in the detail of rubber compound and whatever additives they may use as a mild abrasive, really. it's noticeably better.

Agree on the dura ace pad. It is about as good as it can be. Which is still not great.

Can't wait for hydraulic discs for CX

wow, didnt realize there was life in this thread! i think part of the problem with my setup is that the tektros are made to use v-brake holders with screw mounts, rather than road pad holders, and as such can't be set up to contact the rim cleanly.

if i wanted to switch to canti's with road style cartridge pad holders, and not break the bank, what brakes would i want to look at? shorty ultimates would be within my budget, what about alloy TRPs?

I switch last year from TRP 950 to Avid ultimate. I like the avid more for power and ease of adjustment and installation. I also upgraded the TRP to road holders and still the power was not as good as the ultimate. Of course this is base on feel so I can not really confirm the power relative to each other.