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Sounds almost like an Interdiction Matrix stop use on in that area if it is effecting everything in a certain area. But if it started happening right after you turned on the forestry farm have you tried breaking it?
You can use the new version of the GC which might have some luck.
http://forum.feed-the-beast.com/threads/jvm-arguments-for-modded-minecraft.28994/#post-397367
There is quite a bit of that spam on my server also, but I don't notice any lag via it. If your convinced it is causing lag you have the coordinates of the block in that message.
Um well it use to just be a visual glitch. If you relog and its still there then it someone did delete that block.*On firefox can't edit and I butchered what I was trying to say
If you relog and its still there then it did get deleted somehow.
If its not working then you know there is something wrong. I would check using a vanilla server just to make sure something else is not causing the issue.
Well what OS is your server running on? I would double and tripple check the port forwarding as that should be the only issue (unless your on windows you might just need to run it as admin)
A few mods changed names so just replacing the ones with the same names will not work. Delete your Coremods and Mods folder then extract the new ones in.