This has been reported before to me and was exactly as CaptJosh explains, it appears to happen on a mission restart. I wasn't ever able to come up with a possible leak but figured that it was bmpman's caching system. Between missions it doesn't unload graphics from memory to make reloading the same, or loading the next, mission considerably faster. The problem seems to be how much data can be in bmpman at the time and during a reload it can cause systems without quite enough free memory to hit swap a lot causing a big slowdown either on load or in mission as it pages back to system memory.
Reducing the memory being used by either not using some options (such as -glow, -pcx32, -d3dmipmap) and/or making sure to have as much free RAM as possible before you play the game, should give the same results as disabling the bmpman caching. Also try to use memory saving things like -loadonlyused and not using AA with your video card. The reintroduction of -img2dds will also help out a great deal with memory usage for those who can deal with the lowered image quality due to compression.
I haven't heard yet as to whether or not disabling bmpman caching fixes it (someone was going to test that) but I am going to add a cmdline to enable it and have it disabled by default. I may also add the ability to turn it on automatically if there is plenty of free RAM when the game loads but that's for a later time.