I had a look at the problem again and sorry about the incorrect direction that I've pointed you to. Please ignore the post above.
You are possibly encountering two problems at the moment:
1. Unable to export >1000 issues
2. Export to Excel doesn't export all records only from the current page (similar to the issue that you have linked)
In order to rectify the first problem, please refer to JRA-8214. The reason exporting more than 1000 issues is possible in your previous version is because tempMax was set to 10000. However, in 3.6.2 the value is only set to 1000. You may edit this value to by following the steps defined in the given link.
Regarding the second problem, it may still be a bug at the moment which is currently being tracked at JRA-8899. Please cast your vote in order to get it fixed or add yourself s a watcher for future updates.
Hope this answers your question. Let us know how it goes and please contact us if you have further questions. Thanks!