I have never heard of that - I use LogTenPro too, and has never been an issue so far in EASA land.
I did have a problem, though, in Africa. The Kenyan CAA refused to accept my electronic logbook, even when printed out. I had to get a secretary to laboriously transcribe all my records for last six years into a paper logbook. Ironically, the KCAA also insisted that I give a highly detailed breakdown of all my hours such as night PIC cross country by every class of aircraft and hoc - with a paper logbook extracting all this information is almost impossible, but it is a breeze with an electronic logbook.
I am always a bit surprised to find pilots who still use paper logbooks these days. Electronic is so much better. With LogTen Pro you there is even an add on app called "Flight Timer" which uses the iPad sensors to detect when you start taxi, when you take off, when you land, and when you shut down the engine, and then exports the times and ICAO codes directly to your logbook. Far more accurate than trying to fill out your paper logbook at the end of a long day when you can hardly remember where you've been, let alone the timings.