Incorrect Time in PHP despite Timezone

Today I was configuring a server's system time, the server was an Amazon one and after setting the php.ini file's date.timezone field I found a perplexing output from running php's date functions.

The time was off by a half hour!

This was quite odd since it wasn't a whole hour. After thinking a bit and checking the php.ini settings, I looked at the date.default_latitude and date.default_longitude fields. They were set to somewhere in turkey. Editing these two fields to point to within the same timezone as the one I had set caused the time to switch to the correct one.

Very strange! According to the php documentation, those configuration settings only effect the sunrise functions. Apparently not!