@ursitesion We also had a similar problem after we migrated our MySQL DB from Windows to Linux. We were lucky that our table names were already in small caps, the only issue we faced was that inside our application & some Stored Procedures (SP) we had mentioned the table names in Large Caps / Camel Case.
We followed the following steps and were able to solve our problem:
1) Edit the MySQL configuration file (i.e. /etc/my.cnf), and add the following line in [mysqld] heading.
Note: By running the 'mysqld' with lower_case_table_names=1, the database creates the tables in all lower-case names. The existing table names are unaffected.
2) Restart the database so that all database table names are now created in lower-case.
3) Verify that the change we made above did take effect in the database using this query
SHOW VARIABLES LIKE '%lower%';
The instructions are also mentioned here .
Now all our tables are in small caps (which was the case even before we made the change) & queries having table / SP names in large Cap work fine.
Just in case you have your table names also in CAPS this link might be of help (i have not tried it)