Screenshot showing both cases in Special:ExpandTemplates
Bug 529 added the "feature" of adding a newline to templates when they are not at the start of the line if they start with wikitext which has to be at the start of the line (tables, lists, etc.). When using a plain template or invoking a module directly, this works fine. However, when using a template which invokes a module, the newline is ALWAYS added, regardless of if it is necessary.
This often results in nasty <p>s coming along and ruining everything, like they always do. :(
This is easy to test: create a module and a template which starts with a list or table. When using the module through a template you'll always get an extra newline, unlike direct invocation or plain templates, which only add it when necessary.