From the bash man page :

The cmdhist shell option,  if enabled,  causes  the shell  to attempt
to  save each line of a multi-line command in the same history entry,
adding semicolons where necessary to preserve  syntactic correctness. 
The lithist shell option  causes  the shell to save the command  with
embedded newlines instead of semicolons.  See the  description of the
shopt builtin  ...  under  SHELL BUILTIN COMMANDS  for information on
setting  and  unsetting  shell options.
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dug into it and here is the gist:

optional feature of Bash history filtering that isn't always  enabled
by default in distributions is cmdhist. This determines whether multi
-line commands are stored in the history as a single command (on)  or
not (off; default). 

To enable this feature, you would type

      shopt -s cmdhist

To disable this feature, you would type

      shopt -u cmdhist
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not sure if this fixes the prob ... update: script and alias(s) work with cygwin as well