In 5.5.1 JPA Reverse Engineering wizard, the first dialog page asks you to enter the Java src folder and Java package. The third dialog (Configure reverse engineering details) lists the tables to be processed. If you select a table, the Table details on the right expose a Class name: textbox. Unexpectedly (in my mind since the first page already required me to enter the package name) this textbox only works if you type in a fully qualified Java classname. Type in only the last element of the name, and the generated class goes to default (no package). Any table that you do not enter your own class name for is generated in the intended package location.
This could be a very badly documented feature, but my guess is that it is a bug. The content of the textbox should be prefixed by the package name entered on the first dialog page. If the name appears to be qualified (has a “.”) then there is some justification for the current behavior, but unqualified names entered into this box should go to the intended package.