I have a private modpack that contains this mod. I updated this mod to 1.7.8 then to 1.7.9 along with The Erebus, Special Mobs, and PneumaticCraft at the same time. After updating to 1.7.9 I started to notice an issue in which the exact same items were not stacking, until I throw both on the ground and then pick them up. Looking at the metadata via NEI revealed they are the same. I am not sure if it the issue is a result of this mod or another.
Here is the modlist of my pack.

Is it limited to certain items, or all items?

It's been multiple items and seemingly random. Carrots, torches, obsidian blocks. Also, the glitch may cause me not to be able to put an item in a drawer. Even if the drawer is locked without items in it already.

Well, I can't say that anything in 1.7.9 would cause this. 1.7.8 included a lot of changes item handling, mainly in the controller. But 1.7.9 was a tiny bugfix exclusive to the controller.

If an item and its metadata are the same, then the only thing I can think of off-hand is that something started adding tag data to items. If the tags mismatch, the items are considered unequal. Think things like dyed leather armor.

Try taking a look with something like InvEdit or MCEdit.

Oh wait, you mentioned this applied to 1.7.8 too. If it's a controller issue specifically, it's worth more investigation on my side. But if you're having troubles putting into drawers directly, then then 1.7.8 changes shouldn't have affected that.

I haven't been able to reproduce the issue at will, and I don't think that it explicitly happens with drawers or controllers as I can just find items out and about and they will not stack. I appreciate your suggestions regardless. If I do come up with a way to consistently reproduce the issue, and it does involve the mod, i'll let you know. Again thank you.

I know it is out of line at this point, but I used your NBTEditor and I found that your assumption regarding tags was correct. In at least one instance of items not stacking I found this which are two stacks of 4 Nether Redstone Ore that will not stack. One has a tag and another doesn't. Do you think that is the issue and would you have any idea how I can figure out what mod is doing it?

I have no idea what mod is causing it. You might be able to ask around on MCF or FTB.

But yeah, that "feature" is going to cause a lot of havoc with item stacking everywhere.

Alright, well I think we can consider this closed on your end. Again I appreciate the assistance.