Rasberry,
You've hit on one of the great imponderables - and weaknesses of Astrology. The oldest form of House system appears to be whole signs - that is if you were born with any part of, say, Leo rising then the whole of Leo became your first House.
This was probably followed by the Equal House System - if 23 degrees of Leo is rising then all your House cusps are 23 degrees of consecutive signs.
Such systems are simple and don't cause that much confusion - though the two of them obviously don't necessarily produce the same House placements. So as soon as this second system of Houses began to be used the problem you mentioned had arrived.
From around the 13th Century other systems have come into Astrology - Placidus, Regiomontanus, Campanus, Koch, etc. Unlike the first two systems these all have the MC as the cusp of the 10th House as well as the Ascendant as cusp of the first. As they differ in how they divide up space and time they produce different results, for the intermediate House cusps (2/8, 3/9, 5/11, 6/12). Often the difference is such that planets are in the same house under several systems but, as you point out it is quite possible to have significant differences.
Does it make a difference?
I've tried interpreting the same chart using different systems, and the end result was very similar, though often the same conclusions were reached by a 'round about route'. Also bear in mind that adjacent Houses are not unconnected - there is usually a theme which can connect them.
I've also seen some Astrologers argue that some systems are better for some tasks than others. So they may use Placidus for natal work and Regiomontanus for Horary work.
I tend to use Placidus for natal work, unless the birth is very northerly and then I use Equal House. For Horary, I use either Placidus or Regiomontanus (which was used by William Lilly, the great seventeenth century Astrologer).
