crash report:
http://paste.ubuntu.com/p/z48t2NVZjc/

fml server latest:
http://paste.ubuntu.com/p/Wsh3w7MyGd/

Hey there and apologies for disturbing the peace here. I attempted to silently fix a shortcoming and push a PR but didn't got past OP's issue after forking and building the project:

If my guess is correct the following error log might look familiar: https://pastebin.com/tM5Zzt5P
The fork runs fine in the development environment (run client - intellij) but fails to run outside the client and results in the above crash whereas a freshly downloaded .jar does work.

The whole reason I have forked this mod is because I'm working on a alternate RLCraft modpack (endorsed by shivaxi) and found out that potentialspawn within the NBT container doesn't tag entities with NBT_TAG_SPAWNER_POS. I wanted to figure out why this was, fix this and PR. Seemed simple enough until encountered the same issue as OP.

Then I blame @Laike-Endaril

Does this happen as well with 1.6.2 ?

I will go test right away then, and take a look at those logs

Edit 1:
Same crash confirmed on Forge 14.23.5.2838 (dedicated), SpawnerControl 1.6.3, no other mods installed. Also confirmed this does not happen with 1.6.2 on my setup, as you described.

That being said, the error is for a missing method in a vanilla MC class...which is being called from a file I did not edit:

Caused by: java.lang.NoSuchMethodError: net.minecraft.nbt.NBTTagCompound.setInteger(Ljava/lang/String;I)V
	at ladysnake.spawnercontrol.controlledspawner.CapabilityControllableSpawner$Storage.writeNBT(CapabilityControllableSpawner.java:119) ~[CapabilityControllableSpawner$Storage.class:?]

Here it is in the code:

I can confirm that the method exists in Forge 14.23.5.2768 (because that's what I've been developing in), but I'm not sure if it exists or not in 14.23.5.2838, and I can't set up an environment for it right now due to a confirmed Forge SSL certificate issue wreaking havoc with their maven. Hopefully it will get fixed soon.

Note: Dedicated is not working with 1.6.3 on Forge 14.23.5.2768 either. Different error though. Or rather, the same type of error, but for a different method (which indeed, does not exist in this version of Forge):

java.lang.NoSuchMethodError: net.minecraft.tileentity.TileEntityMobSpawner.isInvalid()Z
	at ladysnake.spawnercontrol.SpawnerEventHandler.onTickWorldTick(SpawnerEventHandler.java:89) ~[SpawnerEventHandler.class:?]

And in the code:

Again, this is code I did not edit. Did this code get added/changed after the 1.6.2 release? Ie. it happened to "tag along" when my PR got added?

I may have to crack open the release 1.6.2 jar itself and see if this code already exists in it or not. I have a feeling it doesn't though.

Confirmed. I cracked open the actual jar files for 1.6.2 and 1.6.3, and the code in that file differs. I did not edit that code or any files that would've changed how it was built.

Hf @Pyrofab lol

It's just due to the change from SRG names to (now outdated) MCP names in some commits that were never part of a release (until now). They just need to be changed back to SRG, probably. Hopefully there's nothing else in those commits that will break things

Actually, it seems not to be anything wrong with the code itself, but rather the build process? I was able to build my own jar with the current code and it works fine on dedicated, on both 14.23.5.2768 and 14.23.5.2838. Pyrofab and I will work this out on discord.

These (the OP's issue, as well as the additional related one I mentioned) are now fixed in 1.6.3b