I was wondering whether anyone had trouble with using RECON when running REPEATMODELER. 

I have downloaded the latest version of RECON (1.08). When prompted by ./configure in REPEATMODELER, I give the file path of RECON as /$RECON/bin. However, the message "RECON-1.08/bin does not appear to contain a complete set of files". The /bin file is empty, however, do I have to put executable files in it - if so, how do I do this? 

Does anyone know how I solve this issue? 

Thank you 
Have you compiled RECON?

If not, open a terminal in the src folder, then run " make" and then "make install".
Next in the script "recon.pl" in the scripts directory -- on the third line, add
the path to the binaries (the bin directory here) between the double
quotes.

I know this answer is too late for you, but it might help others.
Cheers.