Mono compatibility issues, even for a blank project

[Ehsanit]

As I understand it .net bytecode is standardized regardless of language and any JIT engine should be able to run it. I wrote a program (an encrypted diary) for a friend a few years ago that I now need to modify to run in Ubuntu.
Running it through the MoMA analysis I found it had about 145 points of incompatibility, so no surprises that it didn't want to run. Most of those were because I used legacy Basic functions rather than the managed Object Orientated code, and I'm quite quickly working my way through the list (At the time of writing I have 60 entries in the "Method Missing from Mono" column of the analysis).

However there are 17 issues that don't appear in my code at all; in fact they are detected if I create and compile a brand new windows forms project. I can't work out how to deal with these appropriately. A few examples are as follows:

void Main (String[])
bool WindowsFormsApplicationBase.get_UseCompatibleTextRendering ()

void Main (String[])
void WindowsFormsApplicationBase.Run (String[])

void OnCreateMainForm ()
void WindowsFormsApplicationBase.set_MainForm (Form)

void .ctor ()
void WindowsFormsApplicationBase..ctor (AuthenticationMode)

T Create__Instance__ (T)
string Utils.GetResourceString (string, String[])

void AutoSaveSettings (Object, EventArgs)
bool WindowsFormsApplicationBase.get_SaveMySettingsOnExit ()

Does anyone know what these are, and more importantly how I can fix them.

I've also tried to rewrite the program from scratch in C# under monodevelop, and failed due to critical differences in string handling, lack of experience with that language, failing to get the resulting code to run on Windows, and other things.