The problem is that you're most likely not generating proxies for a sufficiently large number of classes. The way JNBProxy works is to only generate a method if all the parameters of that method have generated proxies. The rationale is that if proxies for the parameter classes haven't been generated, then the method is not of much use.
There are two ways you can address this issue:
1. Using JNBProxy (either the GUI or command-line version), make sure that you have chosen to generate proxies for all classes used in the relevant method parameters. If a class is only used in a method which you do not plan to use, it's not necessary to generate a proxy for it.
2. If you are generating classes from the classpath, make sure that the "Include supporting classes" checkbox is checked. For each class for which this box is checked, JNBProxy will generate proxies for the superclass, all implemented interfaces, and all classes used in fields, method parameters, return values, and thrown exceptions. The proxy generator will then iterate over all of those classes to generate proxies for their supporting classes, and so forth until no more classes have proxies that need to be generated. Depending on the number of "seed" classes, this may create proxies for several hundred classes (the tool will tell you at the beginning of proxy generation how many proxy classes will be generated) and the process will take a few minutes, but the advantage is that you can be sure that all necessary classes will be generated.
It is also possible to use the Add+ button to generate proxies for all supporting classes.
In either case, all the classes used as method parameters must be in the class path.