Hi!
It’s most likely because I suggested to turn off the Execute Shortcodes? option, but it was not the issue at all. Can you please turn it back on and create a new index? If it’s created successfully, then it’s definitely not causing any problems.
When that option is turned on, it tries to strip the shortcodes but leave the content, but for more complex (nested) ones it might not work as expected.
There are also limitations with the index table engine (no inner word matches) you should be aware of, but I highly doubt it’s the case.