This strikes me as expected behavior rather than an issue.
The ISO 8601 datetime format
2018-09-13T09:01:00Z breaks down like this:
- Year: 2018
- Month: 9
- Day: 13
- Hour: 9
- Minute: 1
- Second: 0
- Time zone: Z (i.e. "Zulu" time, UTC+0)
The time zone is the key here. When you specify the datetime in the other format (From what I know, DBAmp uses T-SQL) you've listed
09-13-2018 09:01:00, the timezone is not present, and the DBAmp documentation makes it sound like it assumes you're specifying local times by default.
If you're not in the UTC+0 time zone, then it's not at all surprising that those two different queries would return different results, because you are actually querying for records that fall under different datetime ranges
Probably the easiest solution here is to adjust your "openquery" SOQL query to specify your timezone. If I were doing this, being in Minnesota, USA where we're currently UTC-5, the datetime string I'd be using is "2018-09-13T09:01:00-0500"
Adjust according to your own UTC timezone