You forgot a major mod update. Sure, it's not a mod most people use or know about, but the improvements are pretty major :
Notice how the latest version for immibi's mods is "50.1.3". 49.1.2 is the version you derped and included in 3.1.3. Oh noes!
Here's the list of changes SINCE the version included in 3.1.3 :
Also, here's a BIG ONE : A DUPING BUG. That's right, ANYONE can dupe using the unpatched retrievulator in Tekkit 3.1.2. Most people don't know about this bug, but it lets you dupe anything. Just put a retrievulator down, stick something into it, BREAK it using either a block breaker, EE tool, OR IC2 miner (all 3 will dupe! most server admins don't know this!), and it dupes. Easy to do, anyone can do it.
So if you don't fix this, everyone will be able to dupe. Great job, Team!
Here's the changelog of all the updates you are missing :
Note: I sometimes forget to update this right after updating the mod itself.
Fixed not working on dedicated (non-LAN) servers
Updated to MC 1.3.2.
If any exception is thrown while trying to add the retriever jammer to the IC2 recycler blacklist, it will be silently ignored instead of crashing. Retrievulators now always stop emitting a redstone signal when there are enough items in the target inventory. All blocks are now non-solid and will not conduct redstone. Retrievulators can be placed adjacent to each other without causing problems. Retriever jammers on the ground will disappear if you walk over them instead of being picked up. Retrievulators will slow down after some time without any items passing through them. Retrievulators can be rotated with screwdrivers (including sonic screwdrivers) Added storage blocks. Added config option to disable retrievulators.
Fixed BHC shift-clicking Retrievulator now uses fake slots, similar to the Logistics Pipe ones, in the T area. Important: Existing items in this area will become fake items and you will not be able to get them back! Right click to add, left click to subtract items. Shift to go faster. If the slot is empty, click on it with any stack to copy that stack.
Fixed retrievulator orientation in SMP Removed debug message Added retriever jammer to IC2 recycler blacklist if IC2 is installed (this means if you recycle one you have no chance of getting scrap) Allowed BHC to be enabled with the config option in SMP.
Fixed chunk resets caused by black hole chests.