Hello,
I also have this same issue so I will share my efforts so far; hopefully we can think of a solution together! To add one additional factor outside your setup, I downloaded Thaumcraft 3.0.3 for my server as well.
So far, I have verified the difficulty, mob spawning is true, and game is set to survival mode. Additionally, I spun up a new Big Dig server and pushed my world data into it to try and rule out mod configuration as the possible issue. As expected, there were still no mobs. I also read that view distance could be culprit, and found mine to be set to 10. I set mine to 7, and then back to 10 just in case. Still no mobs. I can only guess that somehow the world data itself is bugged (consistent with your experience that this happens regardless of mods/packs) , but I have no idea how to fix that. I was thinking of possibly using something like this to add commands to the server to kill groups or all mobs: http://www.minecraftforum.net/topic/1592223-wip-alphaforgeessentials-permissions-protection-logging-more-for-forge-based-servers/ However, the mobcap doesn't really seem to be the issue.
The F3 debug screen indicates that where I'm currently standing is not mobcapped. Check out this documentation for a primer on reading the screen: http://www.minecraftwiki.net/wiki/Debug_screen
"E (second row) Number of rendered entities over total entities"
Mine currently reads 19/55, not indicating a mob cap issue.
OR possibly find a Forge compatible mod that provide some mob spawn tweaking options. Other than that options seem to be make a new a world. Obviously that's not ideal as we'd have to start over, and the issue could likely happen again.
This video seems to have an interesting solution as well:
- I plan on trying this next, will post again if I find a fix.