In Freemodus, the downloadspeed is limited to 20-200kb/s. After 100MB you have to wait up to 15 minutes to download the next file. Sometimes it looks like jd would download “Block” after block. This is due to rapidshare's bandwith limitation. This screenshot is taken from the tool “Netlimiter” while downloading in Free-mode with firefox. YOU can clearly see the peaks followed by a few seconds without transfer. This is a totaly normal behaviour.
This a a rapidshare freeuser restriction. If a lot of users are trying to download a certain file, it may occure that rapidshare asks you to wait 2 minutes. JDownloader tries to reconnect or retries to download after 2 minutes.