On further investigation, it appears that there are differences between various S3 devices (or operators, or Android versions). On many S3 devices there are no problems with the GPS. Voyager detects a GPS fix in a matter of seconds, and signal is not lost even when switching to Google Maps. I tested this myself on an S3 with Android 4.1.2. Still don't know what causes the problem with some other S3 devices.

Could you please send this information about Galaxy S3 issue to Samsung. May be they could advice any way out. It is really important and convenient to have GPS navigator and your soft working simultaneously.

We're still investigating (through various logs sent by S3 owners, and testing other apps). But, if this turns out to be a phone firmware problem, we can't do anything to fix it.

You plan to solve this problem?

This seems to be a Galaxy S3 issue, as other camera apps behave the same way (apps which can use the camera in the background, too).