Could legitimately be a different strain. DRC has
been the source for other outbreaks. Then again, it's
worth pointing out that the strain determination was
made by the Ugandan government lab. If faced with the
choice of admitting that their containment wasn't/isn't
as effective as they've claimed, or fudging the
determination, so it looks like it just popped up
coincidentally, Uganda might choose the latter. After
all, they both have identical symptoms, containment
procedures and treatments. Add in the fact that the
mortality rate is closer to the values quoted for Sudan,
and you have to wonder.

[link to en.wikipedia.org]

According to the distribution diagram, in the above link,
Bundibugyo ebolavirus has only been seen in south western
Uganda. It is also has one of the lowest morality rates.
Making it a good choice as a "separate outbreak".