Hi,
Thanks for your message. This is a known issue and is not a bug. Meta Box needs a way to detect if the table exists and create a table if not. Internally, Meta Box uses the dbDelta function which does the job. This function causes the issue that you see.
To eliminate this issue, a simple way is that you run the code to create a custom table only once. When the table is created, you can remove that code from your theme/plugin. The plugin will work well as the table is existing and match the fields.
Alternatively, you can create the table manually (via SQL) and remove the code to create custom table in your theme/plugin.