Title says it all. Not sure what's going on, though my guess is the piston is between the extended and retracted states when it gets loaded/unloaded. Strangely enough I've got another hopper timer nearby and that one has never broken like this.
I could try, though I don't think these mods are the problem. They just add features to my HUD so I don't have to search for them (ex. potion/beacon effects in the inventory screen or armor durability). I just happen to notice this problem happen twice within a day or so. It doesn't happen every time I check the timers. (And I've also had times where somehow I have 2 redstone blocks in my timer, so I'm confident it's not something client-side, or at the very least something entirely client-side) I have had issues with pistons in the past. I've noticed that if I leave my (cobble)stone generator on and leave the area, there is a chance that it will break when loading that area up again as somehow the piston will push blocks through an immovable block.