Did you ever resolve this? I am running "Run MaxEnt: Spatial Jackknife" and it seems to run fine, but the output folder has no .bat file...it has 3 temp files and all the All_Occ files (.cpg, .dbf, etc) but nothing else.
I have updated Java, am running Arc 10.6, and both my own data and the sample data work fine through the Maxent Gui, but running Maxent through this SDM seems to work fine, but gives the 'script executed' message after only 10 seconds and the output folder does not contain a .bat file.
Since I can use the Maxent GUI, this isn't the end of the world, but all the other SDM scripts work great so I'd love to try this tool so it would automate the model selection.
Thanks for any insight!