You would have to ask Cyberlink why the menu duration is limited to 99 seconds.
But there is a workaround which may help a little.
Split your 2-minute video into two parts, one of 21 seconds and the other 99 seconds, and Produce these as separate .avi files. Use Part 2 (99 seconds) as your background video on your menu template, and use Part 1 (21 seconds) as a First Play video. Your DVD should then open with the complete two-minute video, with the menu showing over the last 99 seconds of it.
Not quite a 2-minute menu, but close.
HTH
Robert