Check out this forum thread about cases where uneven coverage of NGS seq. (the thread is about Illumina but I think all Platforms have their own quirks)
The consensus is that GC bias and/or enrichment PCR step might be creating platform specific biases.
Whole genome sequencing projects like in
Complete Khoisan and Bantu genomes from southern Africa : Article : Nature where WGS data on different platforms are available have the ability to shed some light on such issues.
So when in doubt, (and have plenty of $ ) sequence with multiple platforms.