Thank you for posting.
There is nothing about a standard FileMaker Pro installation that would corrupt a hard disk. That doesn't help explain what has been happening, but in order to make sense of it, I'll need some additional information.
They may seem obvious to you, but it will be helpful to confirm some details.
1. What installer are you using for FileMaker Pro? Is it a Disc or Electronic Download?
2 There are two downloads available on the FileMaker.com downloads page to update FileMaker Pro 11.0 to FileMaker Pro 11.0.v4 -- what is the file name of the updater you used?
The installation instructions for this is in the Answer ID 9910 (http://help.filemaker.com/app/answers/detail/a_id/9910).
I certainly hope that you don't have a bad hard drive on such a new Mac, but this is, unfortunately, not an outrageous possibility. Please confirm the installers that you have been using and let me know any other details that may help.
The download was electronic and they were both new purchases downloaded from the mail that you send after purchase.
Thanks for confirming that.
I wouldn't be able to reliably reproduce the issue, given it would require having your exact hardware configuration. I see no reason why you shouldn't "trust" your Mac any less that one can a piece of hardware…Time Machine exists for a reason.
That said, I do want to review the steps you took on installation once more; at least, as it should have gone:
1. From FileMaker ESD, install FileMaker Pro 11.
2. From FileMaker ESD, upgrade to FileMaker Pro 11 Advanced (prompted for a qualifying key, the License Key from FileMaker Pro 11 will be entered).
3. Run updater: fmpa_184.108.40.2061b.dmg
4. Result will be an installation of FileMaker Pro 11 Advanced v 11.0v4
If you need any additional help, please let me know.