I have a 3x3 firebox and a 3x3x3 boiler. I run a private server and every now and then when I log in after updating Railcraft I notice that I'm not producing any power or steam and I find that the boiler has become the separate slightly smaller blocks like it is before it becomes a multiblock (as if when the chunk loaded the boiler didn't realize it was a multiblock). The firebox remains as it always is. I have dug the entire boiler out to see if an enderman placed a grass block in the middle (I had read of that happening on the forums) but everything was solid. The fix for me has been that whenever this happens to remove one block, place the block back and then everything works (it pops out the coal so I put that back in). This did not happen prior to the recent update from 7.2.3.0 to 7.3.0.0.

Minecraft SMP 1.5.2 running on Mint (Debian Clone)
Railcraft 7.3.0.0
Forge 7.8.0.716
If you need other versions let me know, I'm running quite a few mods.

I'd look elsewhere, because I didn't change anything between those versions. Try reverting Forge/MCPC+.