The iPad Mini, and previous iPad models before it, have had this type of issue. There is nothing wrong with your iPad; though the message 'not charging' will appear, your iPad actually IS charging, the irony being that it will never indicate its charging unless the screen is locked . All this means is that where your charging the iPad from has enough power to be recognized, and even to charge, but doesn't supply enough power to charge at the expected rate of speed, so it will indicate as 'not charging' to show it recognizes the device, your still getting power/ charging, but not enough that the iPad would prefer. Charging from a USB port that has more power then the one you are currently using will resolve this (example: try connecting to the USB port in the back of your computer tower rather then from a keyboard or monitor). Hope this helps
Good to have it confirmed that this a 'normal' issue. I am charging it using the Ac adaptor via the mains rather than via a computer, which I thought might be a faster option and it still displays 'not charging'. However, as you say, it DOES charge despite this, so all is not lost. Just one of those idiosyncrasies I guess!
The quickest way (and really the only way) to charge your iPad is with the included 10W USB Power Adapter. iPad will also charge, although more slowly, when attached to a computer with a high-power USB port (many recent Mac computers) or with an iPhone Power Adapter (5W). When attached to a computer via a standard USB port (most PCs or older Mac computers) iPad will charge very slowly (but iPad indicates not charging). Make sure your computer is on while charging iPad via USB. If iPad is connected to a computer that’s turned off or is in sleep or standby mode, the iPad battery will continue to drain.
Apple recommends that once a month you let the iPad fully discharge & then recharge to 100%.
How to Calibrate Your Mac, iPhone, or iPad Battery
At this link http://www.tomshardware.com/reviews/galaxy-tab-android-tablet,3014-11.html , tests show that the iPad 2 battery (25 watt-hours) will charge to 90% in 3 hours 1 minute. It will charge to 100% in 4 hours 2 minutes. The new iPad has a larger capacity battery (42 watt-hours), so using the 10W charger will obviously take longer. If you are using your iPad while charging, it will take even longer. It's best to turn your new iPad OFF and charge over night. Also look at The iPad's charging challenge explained http://www.macworld.com/article/1150356/ipadcharging.html
Also, if you have a 3rd generation iPad, look at
Apple: iPad Battery Nothing to Get Charged Up About
Apple Explains New iPad's Continued Charging Beyond 100% Battery Level
New iPad Takes Much Longer to Charge Than iPad 2
Apple Batteries - iPad http://www.apple.com/batteries/ipad.html
Extend iPad Battery Life (Look at pjl123 comment)
New iPad Slow to Recharge, Barely Charges During Use
Tips About Charging for New iPad 3
How to Save and Prolong the battery life of your new ipad
Prolong battery lifespan for iPad / iPad 2 / iPad 3: charging tips
iPhone, iPod, Using the iPad Charger
Install and use Battery Doctor HD
In rare instances when using the Camera Connection Kit, you may notice that iPad does not charge after using the Camera Connection Kit. Disconnecting and reconnecting the iPad from the charger will resolve this issue.