MYSQL error after upgrading concrete5 on a windows server

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I have a few sites running on windows servers that I need to upgrade.

I followed the same process that I have followed on my Unix servers:
upload the new version of concrete5 to the "updates" folder and then go to the updates section of the dashboard.

I just tried upgrading a site running concrete5 5.4.1.1 to 5.4.2.2.

The upgrade took a very long time and never seemed to complete. I am wondering whether MYSQL timed out. I then got the following error in the dashboard:

An Unexpected Error occurred while upgrading: mysql error: [2006: MySQL server has gone away] in EXECUTE("CREATE TABLE ComposerDrafts ( cID INTEGER(10) UNSIGNED NOT NULL DEFAULT 0, cpPublishParentID INTEGER(10) UNSIGNED NOT NULL DEFAULT 0, PRIMARY KEY (cID) )")

When I visited the home page I got the following:

mysql error: [1146: Table 'dv_xxxx.ComposerTypes' doesn't exist] in EXECUTE("select * from ComposerTypes where ctID = '1'")

I was able to get the site back by altering the config file but still need to upgrade.

Has anyone been able to upgrade concrete5 on a windows serrver?

Thanks

The environment details are:

# concrete5 Version
5.4.1.1

# concrete5 Packages
Breadcrumbs (1.0), Database Backup (1.0), Designer Content (2.1.3), Featured Content Slider (1.0.3), Flickrcrete (1.0.7), Pro News (1.3.7), Sortable Fancybox Gallery (1.14), tnSpacer (1.2).

# concrete5 Overrides
blocks/sponsors, css/design.css, css/Print.css, css/structure.css, css/text.css, css/v4WCA.css, css/w3WCA.css, css/w3WCACM.css, css/w3WCAGallery.css, css/w3WCANewWhite.css, themes/detail, themes/home, themes/includes

# Server Software
Microsoft-IIS/6.0

# Server API
cgi-fcgi

# PHP Version
5.2.17

# PHP Extensions
bcmath, calendar, cgi-fcgi, com_dotnet, ctype, date, dom, filter, ftp, gd, hash, iconv, ionCube Loader, json, libxml, mbstring, mysql, odbc, pcre, PDO, pdo_sqlite, Reflection, session, SimpleXML, SPL, SQLite, standard, tokenizer, wddx, xml, xmlreader, xmlwriter, xsl, zip, zlib.

# PHP Settings
log_errors_max_len - 1024
max_execution_time - 5
max_file_uploads - 20
max_input_nesting_level - 64
max_input_time - 60
memory_limit - 128M
post_max_size - 8M
safe_mode - Off
safe_mode_exec_dir - <i>no value</i>
safe_mode_gid - Off
safe_mode_include_dir - <i>no value</i>
sql.safe_mode - Off
upload_max_filesize - 2M
mysql.max_links - Unlimited
mysql.max_persistent - Unlimited
odbc.max_links - Unlimited
odbc.max_persistent - Unlimited
pcre.backtrack_limit - 100000
pcre.recursion_limit - 100000
session.cache_limiter - nocache
session.gc_maxlifetime - 7200
safe_mode_allowed_env_vars - PHP_
safe_mode_protected_env_vars - LD_LIBRARY_PATH

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