I'm sorry to hear that. I'm not having problems with my farms since updating. Perhaps if I pass along some info (lots and lots of info) something of it will be relevant to you and help you some. With Progressive Automation-1.7.10-1.6.16, I built a 9x9 tree farm (iron chopper) to produce wood to make charcoal to power the machines and to make sticks to craft the tools (wooden crafter). Then I made a 9x9 wheat farm (stone planter) to feed cows (stone animal farmer) for leather and steak (stone killer). It was fully automated and self-contained except for the animal farmer (It would not accept inputs via any method other than manual). For that reason I updated to Progressive Automation-1.7.10-1.6.24, and that update broke my set up. None of the various pipes or hoppers I tried were connecting or inputting properly no matter what I tried. Then I updated to Progressive Automation-1.7.10-1.6.27 and everything worked again. I did nothing to the Progressive Automation machines with the PA wrench. I didn't assign values to the sides of the machines. I left them as they were when I crafted them.
I started in my world with Mekanism. The first farm I built was the tree farm. I used Mekanism's Logistical Sorter and Advanced Logistical Transporters to shuttle items to and from a vanilla furnace, to the wooden crafters, back into the PA machines, and finally to an output overflow chest. I was fixated on Mekanism at that point and forgot about other ways to transport items. So, I filled all but one of the inventory slots in the wooden crafters with a single dirt block so that only one slot would be filled with the inputted item. By the time I expanded to the wheat farm, I was heavily invested in Extra Utilities and its Transfer Nodes and Transfer Pipes. I attached a Rationing Pipe to the side of PA's machines, eliminating the need to fill the inventory slots with a dirt block. PA's stone planter dumps seed and wheat into its inventory slots. I have a Mekanism's Advanced Logistical Transporter set to PULL mode with Mekanism's Configurator attached to the underside of the planter, dumping the inventory slots into a chest. I have a Transfer Node and Filter pulling out the seeds with a Transfer Pipe+Rationing Pipe running back up to the side of the planter seen here -
http://imgur.com/FWAo0yh. You can see in that image that I still have a Mekanism's Advanced Logistical Transporter attached to the side of the stone planter. The Advanced Logistical Transporter pipe is inputting the stone hoe into the wooden planter's tool slot (The other end of that Advanced Logistical Transporter is in PULL mode attached to the bottom of the wooden crafter).
tl;dr - I'm inputting to Progressive Automation machines with Extra Utilities Rationing pipes attached to the sides of the machines. I have not configured the sides of the machines with the Progressive Automation wrench. The inputted tool goes into the "tool" slot of the machine automatically (as it should), and the tools do not go into and fill up the inventory slots. The animal farmer accepts inputted wheat as a "tool" into its "tool" slot and does not continue to fill the inventory slots with wheat.