I found the problem... we changed HyperSizer so that it does not generate a CL2 or CP2 with multiple run-decks. The thing is, it really doesn't need to generate these files because these files contain elements which are the same for every run-deck... (the properties and materials files, PM1, PM2 file can potentially change between run decks, so it does need to be generated for every run-deck).
I'm not sure there is a work around in the current HyperFEA because it is expecting the CP2 and CL2 files to be generated... it might need to be updated. We will try to update as soon as possible.
You can always do the process manually... in the second run-deck, simply point to the first run-decks CP1 and CL1 file... like I said, they don'tneed to change from run-deck to run-deck, so it shouldn't be too hard to manually iterate.