I am using Liferay 6.1, Tomcat and MySQL. I have a custom-sql sentence for a list portlet. The custom-sql uses two parameters: an array of groupIds and a result limit.
Perhaps hibernate is quoting your string of groupIds (presumably it is in the form of "1,2,3,4"
and when hibernate translates this to sql it is putting quotes around it for you?
You may want to try something like this (from Liferay itself):
String sql = CustomSQLUtil.get(FIND_BY_C_C);
sql = StringUtil.replace(sql, "[$GROUP_IDS$]", groupIds);
And include ([$GROUP_IDS$])
in place of the (?)
in your SQL