I also had the same issues with script execution errors since upgrading to SAM 6.1. I've just been sent a fix for my case, 607501, that looks to have resolved the issue:
1. Open C:\Program Files (x86)\SolarWinds\Orion\APM\SolarWinds.APM.Probes.dll.config in notepad.
2. Find the line that looks like <LinuxScriptSettings PromptWait="2" ColumnCount="200" TemporaryScriptFileNamePrefix="APM_"/>
3. Modify this line to look like <LinuxScriptSettings PromptWait="2" ColumnCount="200" TemporaryScriptFileNamePrefix="APM_" CreateFileRetryCount="4" CatCommandWait="1000"/>
4. Restart all services in Orion Service Manager.