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IIRC from the textev, Major Phandys is the person who put the iceboat message in the queue - and I suspect he did it at Hauwerd's direction. Hauwerd KNEW that he and his brother would be arrested in the Inquisition's pogrom, and he needed to find a plausible way to (A) eliminate any potential for the Question pulling any information about the reformists out of him or his brother; and (B) protect his network of "loyal" Temple Guardsmen so they could support a potential Temple revolt.
Continuing, I am pretty certain that the textev states that Hauwerd's note to Duchairn tells him about the reformists in the Temple and the network of loyal Guardsmen (rather like "here is a list of names you can TRUST")... Imagine Duchairn's surprise when he finds Phandys' name close to the top of the list. Then it's a relatively simple matter to "feel out" Phandys while continuing to make the pro-forma complaints to the Inquisition about how Phandys should be reassigned to a position where he can give greater "value" to the Inquisition... All the time knowing it'll never happen.
When Phandys and Hauwerd were fighting, recall the statement that when Hauwerd was run through, he looked up at Phandys with a look of gratitude - no doubt in my mind that the fight was pre-planned to kill Hauwerd and also to "protect" Phandys - allowing him to move into an even more important position. He got promoted soon after and assigned to oversee Duchairn.
... His discovery of the iceboat reservation and his subsequent "fight to the death" with Hauwerd and promotion seemed way to coincidental to me... Rather like Master Seablanket (Coris' valet) and how he ended up as a "triple agent." 
