Hi Martin,
Thank you for the heads up on this. This is a known limitation right now. I will be releasing a version today 11/9/2015 that addresses this. The function call will change from saEnableExternalReference to saSetTimebase(device, SA_REF_EXTERNAL_IN). The external timebase will be reset when calling the saCloseDevice function so it should be able to be set again once you re-open the device, without reloading the DLL.
Keep an eye out for that. Version 3.0.9 of the SA api. It will be released with version 3.0.17 of Spike.
Regards,
A.J.