If you're still having issues related to turtles (both normal ones and the boss ones), you can try changing your difficulty to peaceful thru the server properties. Run the server again and if that succeeds, then it's definitely a mob issue (most likely the turtles).
Go into your server's main folder, then go into the Chocolate folder. In the Chocolate folder, go into the Dungeonconfig folder, then open up swampTurtleCave.prop with the text editor of your choice (personally, I use notepad or N++). Scroll to the bottom (if you have to) and find the lines containing "mob = triton" and "boss = 3".
For "mob = triton" change triton to slime or any other mob you'd like to replace it with.
For "boss = 3" change 3 to 1 any of the other available numbers/bosses (shown in the same properties file in comment line ("#...")).
(Note: if you do change to slime and 1, your swamp turtle caves turn into swamp slime caves in a way) (it's a needed sacrifice until turtles get fixed..)
tldr; The turtles are most likely causing the crashes. Either disable the dungeon they spawn in, or turn that dungeon into your own 'custom' dungeon that doesn't have turtles (as long as you don't have triton as the mob and 1 (turtle boss) as the boss in it).
If, in the end, it didn't turn out to be the turtles, then feel free to report any crashes that occur.
If it does turn out to be the turtles, enjoy and have fun!
AND if you need any more help involving the removal/<other action here> of turtles, feel free to ask.