So currently, cross platform (PC,PS3,XBOX360) there is a glitch where your game will freeze for 1-2 seconds everytime you pass a save checkpoint, someone joins your game, someone leaves your game, at anytime anyone saves including yourself.
This is caused if you choose to use the Mission Filter system when you are playing in Vault Hunter Mode.
ChrisF's Response (Community Manager):
Our engineers are investigating the solution here, but until it's resolved we recommend that players avoid using the "Filter" functionality of the Mission List.
So for now don't touch that option even if you are not playing in vault hunter mode (be on the safe side)
This glitch progressively gets worse. At first it will be short 1-2 lags (nothing annoying), but then it becomes 3-5 second lags and it becomes extremely annoying. Many people have reported that eventually if you keep playing on the "damaged" gamesave, your game will fail to load and you game may freeze everytime you attempt to exit the game.
If you are experiencing this problem, STOP playing that gamesave before you do more damage. This only affects the character's gamesave so you can go ahead and create a new character.
Also, if you think removing the missions from IGNORED will help, think twice, after removing the missions from ignored, they will reappear when you reload your game.
ALTERNATIVE REASON FOR CHECKPOINT LAG [FILE SIZE TOO LARGE]
Save files above 60KB start to experience this checkpoint lag. Around 200kb+ the lag gets to about 2-4 seconds (accidentally ride/walk off a cliff while it's frozen). At 300kb+ your game will start crashing when you try to quit. 450KB+ range, one will often crash when zoning into another zone. At 650KB, you will not be able to load your character and the game will crash out with the following error
http://imageshack.us/a/img843/6285/ztkqk.jpg