I seem to be running into a varent of this issue, it only happens sporadically. 
I am running edtFTPNet PRO 5.1
I've narrowed it down to 3 particular clients(out of roughly 50+ we send files to) I am unsure if it is the file content, but it seems to be the file name,
But, when I try uploading/downloading all these files, that error out with the Input string error, they work fine using file zilla. 
It seems any time the filenames have an  underscore"_" or dash "-" I get the Input string not in a correct format error. 
Below are some example file names. 
1813_20081015040342.zip.pgp
CFA.LETTERS.20081016_2915.3616.pgp
NSE.INFORMED.VENDOR.09-2008
I've debuged the code, and the exception is happening inside of the edt library so there is nothing I can do to fix this myself. 
Unfortunately this is in a production environment and none of our clients have test environments I can play with, so I'm unable to turn on the level of logging I'd prefer to send to you. 
Any Ideas of how to fix this?
Thanks, 
Albert