We think we found the bug, and indeed it only arises when the trimmed/truncated sequences are >259 nts. (which is why I missed it in testing, my test data was all 250nts or less)
The fix has already been checked in: BUG: change SSE mode to avoid segfault (#82) · qiime2/q2-dada2@0a5cdbb · GitHub
So the 2018.1 release should have this fixed. But the Q2 team might have some guidance on a patched version of 2017.12, I'm not sure. An immediate workaround would be to keep all truncation lengths 255nts or less.