Hello Jennifer, your most answer correctly identified a problem with Cuffdiff returning red boxes last week. However this week I am using Cufflinks. Under the Biass correction option (Yes) and cached Ref sequence data, the using reference genome only returns "no options available. Last time I used Cuffdiff, hg19 was detected and entered.
Ok, glad you discovered what that problem was. The database metadata assigned to the input acts as a filter for the content of that option's pull down menu (and the genome select menu for certain other tools as well).
Thanks for the follow-up! Jen, Galaxy team