I personally have set up Maschine inside of Studio One 3.5.1 on a Windows 10 machine and it should be working for you. Here are some things to try:
1. In Studio One, go into your External Devices list and remove your MIDI devices. Test for the issue once more and see if you can find a device that is linked to the problem.
2. Uninstall the Maschine VST, manually delete the .dll file from your plug-ins directory, and re-install.
3. Try running your song at a sample rate of 44.1 if you are not doing so already.
4. Uninstall Studio One and re-install. Make sure that you are NOT running Studio One as administrator.
5. Make sure that you have installed all of your Windows updates and give your system a reboot.
6. Try removing your settings files from Studio One. Below are instructions:
Go to Help>Open Settings folder.
Copy the contents of the folder over to a folder on your desktop.
Close S1 and delete the contents of the settings folder with the exception of the user.license file as well as the "Extensions" folder.
Open S1 and go to Studio One>Options (Preferences on a Mac) to reconfigure your settings.
Test to see if the problem is resolved. If it is not, please feel free to copy your settings files back over from the backup that you created in step 2.
*If you are missing presets or Sound Sets after doing this, simply double-click one of your Sound Sets under Documents>Studio One>Sound Sets.
If you continue to have the issue, please submit a support ticket from within your my.presonus.com account and a PreSonus Tech would be more than happy to assist.