I would check if any other logo works in its place, if it does, then your image is the problem. It doesn't care much for extension/format as it does for size/dimensions. 
As for this entry, and its path:
MenuLogo = "Amontillado/graphics/Amontillado_logo.png"
You shouldn't worry too much about its path.
It doesn't require its relative/absolute path, it doesn't even requiere an extension.
Amnesia likes to use its own internal list to locate files, one that it's loaded when you start the game, going through each directory you mentioned in your 
resources.cfg.
By specifying a path for your image, you're just telling Amnesia to first check there. Then if it fails it uses its own list.
Also, when you specify an extension, you are filtering the results to just that extension, cause if you don't, it will try with jpegs, dds, etc.
So it's totally valid to put just 
ts_menu_logo
( MenuLogo = "ts_menu_logo" )
Check the rest of the values to confirm this is correct.
Now, about your 
resources.cfg
Quote:<Resources>
<Directory Path="/amontillado" AddSubDirs="true" />
<Directory Path="/amontillado/maps" AddSubDirs="true" />
<Directory Path="/amontillado/graphics" AddSubDirs="true" />
<Directory Path="/amontillado/extra_static_objects" AddSubDirs="true" />
<Directory Path="/amontillado/lights" AddSubDirs="true" />
<Directory Path="/amontillado/extrasounds" AddSubDirs="true" />
<Directory Path="/amontillado/textures" AddSubDirs="true" />
<Directory Path="/amontillado/extra_entities" AddSubDirs="true" />
(standard Directory include commands omitted here)
</Resources>
All those paths are 
extra/not needed (what's the correct expression for that? to say "these elements are more than needed"?)
You need only the first one, at the top, to get loaded first.
<Directory Path=
"/amontillado" AddSubDirs="true" />
Amnesia does use several entries for its directories but it's only because they didn't want to load the whole Amnesia dir to run the game. But you can for your mod. You're gonna need everything from there anyways.
To clarify the extension/path stuff... 
Let's say I have in my imaginary mod 
/Creatures these dir/images:
Creatures
/rabbit/rabbit.jpg
Creatures
/fish/fish.png
And in my 
menu.cfg I write:
MenuLogo=rabbit/fish.jpg   Results in --> Image not found. No image with that name+ext
MenuLogo=rabbit/rabbit.png    Results in --> Image not found. No image with that name+ext
MenuLogo=rabbit/fish    Results in   --> It shows fish.png 
MenuLogo=cat/rabbit     Results in   --> path fails, it shows rabbit.jpg