Does that grf already exist / is it an update? If so: What's its grfID? Or is it a NewGRF yet unknown to bananas?
How does your bananas.ini look like? What was the output when you tried the --dry-run option?
All I can say so far: it's not a general problem. Musa successfully updated my OpenGFX+Airports to bananas on 1st try.
The directory I uploaded and the musa call looked like
ogfx-airports$ ls ogfx-airports-0.5.0
bananas.ini changelog.txt license.txt ogfx-airports.grf readme.txt
ogfx-airports$ musa -c ogfx-airports-0.5.0/bananas.ini -x bananas.ini -x license.txt -u planetmaker -p BLABLABLA -r ogfx-airports-0.5.0/*
Note that I exclude all files from the release directory which I don't want to upload.
my corresponding bananas.ini (which I excluded from upload):
type = NewGRF
# The name for the content; at most 32 characters.
name = OpenGFX+ Airports
# The version of the content; at most 16 characters.
version = 0.5.0
# Description for the content; at most 512 characters.
# If the description_file key exists, then that file is read. Otherwise
# description_text is used. Please not that with description_text it is
# not possible to have newlines in the description.
#description_file = my_description.txt
description_text = Adds rotations and ground awareness to the default airports
# URL to get to the home page of the content.
url = https://dev.openttdcoop.org/projects/airportsplus
license = GPL v2
# A comma separated list of tags for the content. Each tag may be at most 32
# characters long.
tags = opengfx, airport, snow, rotation
# It is preferred to use the nightly revision as that allows your content to
# be visible by the betas and release candidates of the stable release as well.
# openttd_minimum_supported_version = 1.2 r23456
openttd_minimum_supported_version = 1.2 r22518
# openttd_maximum_supported_version = 1.3.0
# A comma separated list of objects this content depends on.
# The case sensitive comma separated list of usernames of the authors that may
# update this content in the content system. The uploading author must be one of
# these specified authors.
authors = planetmaker, openttdcoop
(Note, that bananas.ini is the only way you can *add* contributor access to the NewGRF entry so that several people can update it)