I've identified the same issue when trying to use the percent symbol (%) as part of the regex formula (e.g., (?<=Trans Cost Adj .*%\$$?)\d{1,2}\.\d{2,2}). It appears fine when opening the datatable where being used as a reference formula however, when executing PAD and looking at the RegEx datatable with the program paused, everywhere a single backslash was used as an escape character there appears two backslashes, including two in front of the % symbol (e.g., (?<=Trans Cost Adj .*\\%\\$$?)\\d{1,2}\\.\\d{2,2}). I tried to use %% and \% with no luck.
Naturally, this causes the search pattern to be altered such that no results are returned. This is the first time I have tried to use the % symbol in a RegEx search in PAD so not sure if it was a previous problem on an earlier version. I am currently running version 2.45.393.24179.