They are generally interchangeable, however...
I would consider "strongly recommended" to be more likely to carry a
connotation of negative consequence if the recommendation is not followed.
Strongly recommended - You had better do this, or else.
Highly recommended- Man, this is great you ought to try it!
Also, "Strongly" may be more likely to be used describe the manner in which
something is recommended, (in a manner similar to which someone may be
"strongly reprimanded" )
"Highly" may be more likely to be used to describe the quality of the
recommendation itself, rather than the manner in which the recommendation is
carried out.