I had this problem very recently on a 1.91 version map creation
In this particular mission
1) It was heavily laden with objects
Which i thought might have added to the problem
2) It was uploaded and tested on a linux server
(I have no idea if this has a bearing on it but thought it best to include this info
3) The killtrigger was rectangular by the way
4) Having tested it, after creating the mp pbo on my machine, the problem was not evident
However it did become evident on the server
The position of the trigger, which happened to be a kill trigger for a spawn protection zone, moved to a centralised location on the map
To the exact same location as an ambient sound trigger and its angle changed also
I got rid of the problem by removing all the triggers and starting again
In hindsight, i thought i may have grouped the kill trigger to the ambient sound trigger by accident, or in some way it had grouped itself to it
I cant confirm this, as i didnt try to reproduce the fault
It would be very interesting to see if this is a bug, or simply caused by accidental grouping of triggers