Don't know. I would imagine the people who say that mean overall GPA.
I can tell you, however, that that statement is bogus. I was interviewed by two different schools in 2002, and waitlisted at one of those schools, and both my science and my total GPA were below 3.0. More important than overall GPA is recent GPA trend.
Many schools use a calculation in which they multiply your GPA by some school-related factor (more competitive schools get weighted more) and another factor which brings it to a number near the typical MCAT. Then they add the MCAT. That total must be greater than a certain number (say 60, for example) for them to interview you. If you fall below this, you get weeded out, unless you have an extraordinarily high MCAT or GPA, and then they look at you more carefully. (In my case, I had an extraordinarily high MCAT.)
For example, say the GPA gets multiplied by 10, plus MCAT. Say you went to Harvard, and got a 3.0, and a 32 MCAT, and the school had a minimum of 65. Let's also say that Harvard had an additional weighting factor of 1.2. That would give you a (3.0*1.2*10)+32=68, and you'd get interviewed.
I don't know if any undergrad schools get negative weighting, and I don't think any med school would actually admit to doing this (or give you their formula), but I can promise you that this is often done as a quick way to filter through applicants (I have that from more than one admissions official). Again, if you have a really high MCAT or GPA, even if you fall below the number, they will usually interview you to see if there is some reason you have an outlying score on the other criterion.
