Assuming the motherboard runs a "standard" ISA bus rate, none of Roland's MPU-401 variants should exhibit timing issues. With a non-standard bus rate, they all can and will, including the MPU-401/AT. If an MT-32 is connected, timing-related issues can manifest as "Excl. Checksum Error" messages being displayed on the LCD.
In addition, other sorts of issues can occur when using an MIF-IPC card in an AT-class or newer system.
See this thread:
http://queststudios.com/smf/index.php/topic,1926.0.html
And specifically this post, for a problematic example:
http://queststudios.com/smf/index.php/topic,1 … 3.html#msg23653