I finally got a call 90min after our scheduled appointment. I was advised on how to work around this issue by doing the following.
1. Click on forms in upper right (For me it appears in the blue bar next to Flags and Notifications).
2. Scroll down to Form 1099-B Wks ("Company Name").
3. If the resulting form find the "Quick Entry Table" and scroll down to the ESPP sale in question.
4. Manually change the value in "Cost or Other Basis" column using the adjusted cost basis.
5. Repeat Step 4 for each ESPP sale.
I'm not sure if this is kosher or not but then again I'm not a tax expert.
It took me 5 minutes near the end of the call to convince them that this is indeed a bug and that they have other customers experiencing the same issue. Ridiculous. They assured me that they'll log the bug with updates. They also assured me that the fix won't interfere with the workaround... but I would take it with a grain of salt.
