If you use the current release of Captivate 2 to make elearning intended for an LMS, then do not use the built-in FTP. Likewise, do not use the current Captivate 2 release with FTP and PENS.
When the FTP box is checked, Captivate 2 makes invalid SCORM 1.2 and invalid SCORM 2004 packages. Under these conditions Captivate 2 puts the required zip-archive root-level files like "imsmanifest.xml" down in a directory structure 4-5 levels deep.
Captivate 2 Elearning Output published with FTP
Captivate 2 Elearning Output published locally
This means that when FTP is used, the resulting zip file that gets transferred to the server is NOT valid, whether it is SCORM 1.2 or SCORM 2004. Adobe was notified of this issue last Fall and confirmed the problem. At the time of this post I can not find a tech note about this issue.
The workaround is to not use the built-in FTP. Instead, use the Publish Dialog to publish for Flash (SWF), select the "Output Options" to Zip files and under "Project Information" select the desired eLearning output format for your package. Finally, after Captivate publishes the zip package locally, use a third party FTP tool or other LMS import capabilities to transfer the valid SCORM package to the LMS. This will give you a better shot at having the package import into your LMS (or LCMS).
Captivate 2 Publish Dialog settings for local publishing of packages
Two final notes on this topic. First, this bug means PENS doesn't really work. The work around there is to "trick" Captivate 2 by publishing to one FTP address, and then configuring the Captivate PENS settings to use an alternate URL that has a valid package staged by other means. For anything other than testing the capabilities of an LMS server, I wouldn't bother with this approach-- it sort of defeats the intended simplicity of PENS to manually FTP and publish twice to order to get a single package to an LCMS/LMS.
The second note is that there may be other issues with Captivate content communicating to an LMS. I've received private email from one content developer about some issues and heard from another contact that other settings may not work as intended/advertised. I've yet to verify these, but will post more information once this can be confirmed or denied.