Ok turns out in my projects I wasn't using the Logic limiter or adaptive limiter on the main stereo output.
I did have it on other busses including stems pre the main output, but these instances don't cause the problem.
Thanks to Loopsinner i took a look at other plugins on the output that could be causing the problem.
I am running a fair few in series including Waves NLS bus, Waves Saphira, Waves SSL compressor, Dorough and lo and behold the culprit
was iZotope 8 Tonal balance plugin. Just bypass it when you bounce and that fixes the problem. The other plugins in the chain don't cause any probs.
For some reason I thought the dead air was always there for any file you bounce in logic, however this is obviously
complete nonsense, it's just certain plugins on the output that can cause the problem
If I identify anymore while doing my bounces I'll update this thread
Thanks for everyone's input
Stephen