You're most likely not importing the license correctly -- I had to do this also and you need to carefully read the instructions emailed to you in the agreement. Once you have your license, you need to strip the header and tail and save the license in a location for MEGAN to find it.
In agreement with karl.stamm. If this does not work I would spend some time troubleshooting and trying to figure out what you are doing wrong -- as a last resort I would contact Dan. He's busy, yet very helpful, but I would try your best to solve the situation before contacting him about something trivial as this.
I just changed from MEGAN4 to MEGAN5 and got a similar problem with the new license. I found out that MEGAN5 doesn't like weird letters or characters like "æ", "ø", "å", etc anywhere in the license (ASCII issues I guess). The log window in MEGAN showed these characters as something else. I asked a new license without any of those characters and it worked!
I don't know if you are still having this problem but maybe others are having the same problem as you and this post might help them.