Video Format on iPad Mini

Dear All,
I am pretty sure this question has been asked many times. My apologies for asking again but when I searched for the keywords "video format" in the forum, I didnt get any hits.
I read on the Apple page that the iPad Mini supports MP4 and MOV.
I converted some AVI files using Bigasoft MKV Converter, which converts nearly all types of movie files, into MP4's and MOV's. iTunes 11.0.1.12 loads both these formats into its library but when I attempt to synch it with my iPad, iTunes says that the synch cannot occur because iPad doesnt recognise the format of the file.
Can someone please show me where this has been discussed before or briefly explain to me how I can transfer my AVI's into a format my iPad can read.
P.S. This is my first Apple product, so please pardon my utter ignorance.
Best regards,
Kenneth Gomez.

Is there any difference between the video supported on an iPad mini vs. an iPad (iPad 3)?
Until today, I would have assumed of course not...but I've got 2 iPad Minis for my kids and an iPad for myself.  There are a series of videos in my iTunes that play fine on ATV and my iPad but when transferred to either of my iPad Mini's don't work.
When I sync to either of my iPad mini's, I see the movie being transferred over.  The mini has less storage space as a result of the transfer as well so the content / data is on the Mini somewhere - but the Video App does not see the video (either by going to the App or going to Usage in system preferences to see what's in the video app).
So the summary is :
-- 2 X iPad Mini's and an iPad 3 syncing to the same iPad library
-- Movie A works on iPad 3, but is not recognized by the Video App at all on either of the Mini's
-- I've tested this on a half dozen different movies, all were created / formatted for iPhone / iPad - all work on iPad 3, those that don't work fail on both Mini's
Any thoughts?

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