Take the time to look a the Flower's hull in the museum or ingame sometime, It's a nice rounded bathtub shape, guaranteed to have most impact torpedos bounce off at any angle... as to why you mag shots fail to explode, a flower corvette has a draft of 5 meters, if you set the running depth to 4 the eel will bounce off and sink.
apart from that, the trick to flower corvettes is to let them sink themselves, see my post in screenshots thread.
If you absolutely feel you have to sink an escorts, take out the most dangerous ones, a proper DD or black swan, leave the trawlers, tugs and flowers alone, they really not worth it.