I'm going to guess that your chip has 16-bit timer registers. That is, it might still be a 32-bit register, but only have 16 useful bits in it.
Something like:
31 16 15 0
+--------------------+------------------+
| RESERVED | Auto-reload value|
+--------------------+------------------+
Fact checking forthcoming (if you have a specific part number that would help me out).
Edit: By looking at some documentation [PDF link], my guess seems to be confirmed:
Edit 2: Since you mentioned which chip you were using, I found that documentation too [PDF link], which contains this handy diagram:
As you can see, some timers have 32-bit autoreload, and some don't. Which timer you've chosen will affect the behaviour you see.