Hey there,
we just installed a JIRA server on a Windows 2016 R2 machine.
Using it about 2 weeks now showed us, that there are several problems that occur in our daily workflow.
The software we are developing uses a ISA server to authenticate. This procedure creates a new browser cookie. In our case, the cookie does use a wildcard domain, such as *.domain.de to be available for different applications that we offer. JIRA is running on jira.domain.de. As soon as the cookie gets created, JIRA doesn't work anymore. For example, if you navigate to a dashboard, the menu section on the left side greys out. You can't click on the icons anymore. Other functions - such as opening a issue - neither work.
If we delete the cookie that the ISA server creates, everything is working fine again.
I hope that there is a workaround for that issue. Currently, everyone of our team uses one specific browser only for JIRA. This isn't a solution that we want to stay on forever.