I have a 9x9 area with a powered spawner (cow) in the center and as soon as there are ~9 cows in this fenced area the spawner will continue consuming energy but won't spawn the cows.

http://imgur.com/WNr33OA

The other blocks are from MineFactory Reloaded (1 Auto-Spawner aside the powered spawner, 1 Grinder, 4 Sewer, Tesseract beneath the powered spawner).

Yes, there is a limit on the number of nearby entities which stops the spawning

Exactly. Entity limit applies, it can be configured in the config file as "poweredSpawnerMaxNearbyEntities". Some additional checks from vanilla may run, too. They can be disabled with "poweredSpawnerUseVanillaSpawChecks" (sic!).

PS: All config values are also available in the ingame configuration GUI. In the main menu select "Mods" or in the pause menu select "Mod Options...", then select Ender IO in the list on the left and click the "Config" button.

Is there a reason it's kept as "SpawChecks" and not fixed to "SpawnChecks"?

This limitation should be mentioned in the wiki.