Trouble Enabling Query Caching on MySQL 5.6?
You are right. Your problem is actually very simple.
In Windows, mysqld is looking for my.ini, not my-default.ini
SUGGESTION
Open Windows Command Line (as Administrator) and run the following:
cd &quot;C:\Program Files\MySQL\MySQL Server 5.6&quot;
copy my-default.ini my.ini
net stop MySQL
net start MySQL

Keep in mind that MySQL was running with default settings and no my.ini
So, maybe the lines above
[mysqld]
query_cache_type = 1
query_cache_size = 50M
query_cache_limit = 2M

should be the only lines in my.ini