The short version is that the more markups you import, the slower the process on marking new text for highlighting... For me this meant a 30 second delay every time I tried to highlight something new... Unacceptably slow...
Initially I was pretty impressed, the markups that were imported looked good. Next I saw my custom markup palettes imported, tho they had a few minor glitches. (The import process does not like commas in the palettes, and broke up some of my markups oddly... I submitted a separate bug report.) I tried using them, but found the delay between marking text for highlights, and the actual marking almost 30 seconds. I found the same problem when trying to highlight using the built in palettes. Erasing highlights was just as slow.
Some things I tried to improve performance included disabling the Internet connection, MERGE INDEX, and then REBUILD INDEX, each of which took several hours to run. I closed Logos and rebooted between most steps. I tried IMPORT DELETE HIGHLIGHTING, then tested using the built in palettes, and the highlighting was almost instant. I then did a IMPORT HIGHLIGHTING. When complete, I closed Logos, rebooted, and was back up the the 30 second delay... I did the IMPORT DELETE HIGHLIGHTING again...
This time, I deleted the Resource Markup files older than January 2010 in my Libronixi 3 directory (after backing them up) before running the IMPORT HIGHLIGHTING command. This reduced the number of my markups to only include Isaiah, since that is the only book I have been working on since January. Testing this time, the delay was only about 2-4 seconds... The size of the import was causing the issue...