I have the latest version of Jaksta Music Miner installed with El Capitan. Track lookup does not seem to work any longer. I can understand that it would not find tracks for some of the songs but it has not found any for the last 30 to 40 albums that I have downloaded.
Can you try this beta version:
Let us know if it works for you, we are looking at releasing this update shortly.
I got your email. Does this skip problem only occur with Hoopla? Jaksta Music Miner should still work for video sites such as YouTube (though it will only capture the audio part).
The next time this occurs, can you send us the log file? You can find it by going to the Preferences and clicking the Find Log File button.
Spotify have changed their streaming methods recently, I believe Pandora have too. We have a solution on the way for capturing from these, in fact it is almost ready.