First of all please make sure that you setup the module according to the documentation. For each Plugin you find a documentation directly in our github repository. In every plugin section you find a direct link to the documentation that explains how the plugin needs to be integrated correctly.
If you are sure that the plugin is installed correctly then the main reason for missing payment methods are discrepancies in the amount. They normally stem from discounts that are not correctly transferred to wallee. Make sure that you are using a supported discount plugin. In general the default discount plugins of the shopping cart is supported.
The list of supported plugins (if any) can be found in the FAQ Section of the documentation or our support can help you with a detailed list of supported plugins.