We are having a similar issue as follows:

Customers that are Tax-Exempt are occasionally being charged tax when they should not be. This bug only appears on invoices created using the App, and only occasionally. Sometimes it works, sometimes not. We do not have the problem when creating invoices from a PC browser.

Additionally, invoices created on APP only have some - but not all - invoice customizations.

Come on intuit. This should be a priority but does not appear to be.. 

Like others, we are now actively seeking alternative platforms and will thus be taking our Payment Processing and subscription revenue elsewhere unless this bug is fixed soon.