April was a long time ago, it is probable there are bugs in the version you have that have since been fixed. It sounds like you built your custom features against mojoPortal release dlls instead of source code?
I recommend you checkout mojoPortal trunk from svn then copy and rename one of the solution files and add your custom projects and build against the source code. This way you can stay up to date with the core by doing svn update.
Your custom code will probably not compile against the latest mojoPortal code so you will have to fix some things due to some renaming that has happened. Things like .SiteID .PageID, and .ModuleID are now .SiteId, PageId, and .ModuleId to match FxCop recommendations.
Also if you use the DatePicker it has been renamed to DatePickerControl. If you run into other errors compiling against the latest mojoportal code just let me know and I'll help you solve it.
I think if you get your code working and tested against the latest code in mojoportal svn trunk it will likely solve the problems.
Hope it helps,