In my script I had this:
put %WindowsPath% %FileName%
If i change to 
put '%WindowsPath% %FileName%'
I just get another errormessage:
2017-01-04 14:06:05,107 DEBUG ProcessTrigger [] stdout: DEBUG [ScriptEngine] 4 jan 2017 14:06:05.106 :  Running command: 'put 'C:\ProgramData\Enterprise Distributed Technologies\Complete FTP\Users\MHTEST1\KOO3XLIFE_2015113013574700528.TXT KOO3XLIFE_2015113013574700528.TXT'' 
2017-01-04 14:06:05,111 DEBUG ProcessTrigger [] stdout: DEBUG [ExFTPConnection] 4 jan 2017 14:06:05.111 :  Attempt 1: Distributed Overwrite 
2017-01-04 14:06:05,114 DEBUG ProcessTrigger [] stdout: DEBUG [FTPConnection] 4 jan 2017 14:06:05.114 :  UploadFile(C:\Program Files (x86)\Complete FTP\Server\'C:\ProgramData\Enterprise,Distributed,Overwrite) 
2017-01-04 14:06:05,183 DEBUG ProcessTrigger [] stdout: ERROR [FTPClient] 4 jan 2017 14:06:05.183 :  Failed to open file 'C:\Program Files (x86)\Complete FTP\Server\'C:\ProgramData\Enterprise' 
2017-01-04 14:06:05,183 DEBUG ProcessTrigger [] stdout: ERROR [FTPClient] 4 jan 2017 14:06:05.183 :  System.NotSupportedException: Den angivna s?kv?gens format st?ds inte. 
In english :
The entered path format is not supported.
And also errormessage:
Failed to open file 'C:\Program Files (x86)\Complete FTP\Server\'C:\ProgramData\Enterprise'