There are two possible workarounds to this:
1. Change the transaction definition in SE93 and mark the checkbox 'SAPGUI for HTML'. This will allow the transaction to be started from the Easy Access Menu. I'm not sure if this will have any adverse effect. At first glance there doesn't seem to be anything out of the ordinary about this transaction but thorough testing will tell if all the features you need are still OK through the browser.
2. If you exit SMEN by entering /n in the command field, you will be in transaction S000. From here, LI21 can be started without a problem. Perhaps it would be possible to create your flavor starting from S000 instead of SMEN?