When you tried to install a packaged application, which schema it said it will install to? The message should be displayed right before "Install Application".
I tried to install the packaged application myself using an APEX account which has the SCHEMA2 as default. It still chose the SCHEMA1 by default. My take here is that this seems to be a limitation.
Meeting Minutes Application Express Accounts WORKSPACE1 SCHEMA1
To work-around this, I install the packaged applications from the download files (fxxxx.sql) which can be found under APEX installation files (Downloads\apex_4.2.2_en\apex\core\packaged_apps). (Make sure choose the one compatible with your APEX version.) Just install it as you import an application file. During the import, you will have an option to choose which schema to import to (under Parsing Schema drop-down list).
Hope it helps.