If a MediaWiki template parameter string contains an equals sign, everything before the sign is taken to be the name of the parameter. If it does not contain an equals sign, the parameter string is assigned to the next available numeric parameter.
Thus, the simplest workaround, if you actually want a numbered parameter value to contain an equals sign, is to explicitly number it, like this:
{{ Test | 1 = R = 3/(2-(1+1)) }}
This will cause {{{1}}}
inside the template to expand to the string R = 3/(2-(1+1))
, just as:
{{ Test | equation = R = 3/(2-(1+1)) }}
will cause {{{equation}}}
to expand to that same string.