I've damaged enough switches to know you have to get in there hot and fast, with just enough solder to fill the pads and no more, and work in a pattern like tightening a pipe flange.
Thanks for all the good info in here, I was having a similar issue and found the problem with the help from this thread. After I realized I wired the out cables wrong (didn't cris-cross them) I had to clean and reflow the pins to the secondary board. I cleaned the main board really well but was too excited to try the pedal out when it finished and completely ignored the secondary board's acetone scrub down.