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Custom Profile Installation Hanging

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At my job we have our own profile that we've created using the most recent version of the profile exporter (v3). Recently we added some new features including some repeater matrix fields to the site that the profile is based on, and re-exported the profile. Now when we go to install the site (submit the database configuration details), the installation times out. I tried upping the timeout in php but it just chugs and chugs. I tried installing using both the current master (3.0.148) and the current dev (3.0.153) version.

The blank profile that comes with PW installs no problem.

One point of interest here is that we typically use InnoDB for our sites, but the site that is the source of the profile was MyISAM. I tried installing the profile using MyISAM, and it WORKED. So my thought was that maybe if I converted the profile source site to InnoDB and re-exported, then I could install the site with InnoDB. Unfortunately, after doing so, now I cannot install the profile with either InnoDB OR MyISAM (both just hang).

Any thoughts on what could be at the root of this, or some way that we could troubleshoot it?

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