Rich and I just hit a problem, but luckily it's one with an easy solution.
As discussed on the Maxent discussion group, Maxent version 3.3.2 does not necessarily like underscores too much. Since ENMTools generates replicate names using underscores, this leads to replicates crashing, often with "number format exception" messages from Maxent and "Can't open ..." messages from ENMTools. Steven is aware of the issue and is working on it, but for now we'd suggest sticking with version 3.3.1 for your ENMTools runs.
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