Hi!
Thank you for the excellent answer Neil. I just wanted to explain what the underlying problem was. TimeTable needs to start at 0 in the time (first) column in order to be valid. SystemModeler previously was a bit more lax and allowed it to start anywhere, like in the InvertedPendulum model, even though this meant that the table values at the start of the simulation was undefined. As of SystemModeler 5.0 this is no longer allowed which caused the error above.
It seems like you've already solved the issue with Neil's help, but the download has been updated to reflect your issue. Some other small changes were also updated to better target newer versions of SystemModeler, they could possibly fix your animation issues, though I cannot reproduce them.
http://blog.wolfram.com/2014/11/07/using-arduinos-as-systemmodeler-components/