I have experienced the following:
When my Mk3 is hot, it will not recognise the disc. I believe this is a sign of the laser getting old. By hot, the Mk3 runs at around 40 degrees C (measured on the nav internal diagnotics)
When the car cools a bit - through driving - the disc is recognised.

So to maximise the capability of your nav to read a disc you should do the following:
1. Clean the laser with a cleaning disc that uses the wet cleaning method (with isopropyl alcohol etc).
2. Clean the map disc - this ensures maximum ability to read the disk. Ensure disc is not scratched.
3. Use an original map disc (not a copy).

All of the above helps the laser read the disk.
If your nav still has trouble reading the disk, then a new laser may be required. Realistically it is easier to replace the whole nav unit with a 2nd hand one then find a replacement laser :-)