I am talking Komplete 10U drum kits. There are several of them in kontakt format in this bundle. One of their drawback is that the included midi drum loops can only be played in their respective drum set.

So I had copied all the different midi patterns into a single folder and had the sonar browser pointed to the folder. Yes the browser would play the midi pattern via each kontakt drum. BUT there is a catch. It will not loop correctly. In this case an extra 16th or 8th beat is added to the loop. Like a 4/4 meter now being played as 4/4 + 1/16. We all know that as musicians this is a major PITA having to listen to this.

Any ideas or workaround?

You know you can just drag the grooves from the Native Instruments "Drummer" instruments directly into Sonar though right? In the top right corner of the window in the box titled "GROOVE" there is a little four-way arrow icon in the bottom right of the box. Whichever pattern you have selected, you can click and drag from this four-way arrow icon directly onto a MIDI track. 
 
The clip that appears in the MIDI track will end on the last hit of the pattern, which means that the clip lengths will invariably be a little short of the measure line. Just drag the end of the clip out to the next measure line and they will loop properly. 
 
Incidentally, you can use these clips with other drum instruments too. If you go to the "options" tab at the bottom of the window, there is a section titled "MIDI MAPPING." Open the "Preset" dropdown menu to see a selection of mapping options - you can select GM (General MIDI), Superior Drummer, Addictive Drums, EZDrummer, BFD and a few others. You can also create your own mapping using the note selector and articulation menu below the preset menu. One you've selected your required mapping, any patterns that you drag to your browser using the dragging method described above will be mapped accordingly.