CHeck the advice here
http://www.gnutellaforums.com/306179-post17.html about connection with the new version.
Oh .. you installed the new version separately. Normally LW will remove the previous version at the beginning of the installation process.
Problem is, all the download information is stored in the download preferences called Download.dat & .bak. If you have started a new list in a new incomplete folder, then the new preferences won't have any record of how advanced the other incomplete files are if you moved them across. So I guess you need to make a decision, keep the new download prefs or use the old ones. To use the old ones you'd need to move ALL the files from the old incomplete folder to the new one & replace the new incomplete prefs, in which case you will lose records of your new incomplete files. SO it's realy a choice between one or the other.