Yes, There Are Differences
The % notation is meant to be additive, as percentage points (in the regrettable gaming 'tradition' of conflating them with percents). For example, an Advantage with a base cost of , a +50% enhancement, a +25% enhancement, and a -100% limitation, will have a final adjustment of (+50%+25%-100%) = -25%, and so its final cost will be ¾ of its base cost, that is . This is described on B101 under Modifiers.
A multiplicative cost adjustment (which is much rarer, almost always a special case for a specific trait, and described in the trait in question) is meant to stack purely multiplicatively. The box on B36 explains this in the context of Allies, but the principles should up in some other cases. While the page doesn't spell it out explicitly, the practice supported by actual builds, chargen software etc. is that a 2× and a 3× modifier would result in a final 6× modifier.
In even rarer cases where the two coexist on the same advantage, you should first apply all multiplicative modifiers to the base cost, then apply the final percentile (percent point based) adjustment to that.
Example: Suppose before the game started your has bound a spirit who will show up when called and do your bidding once, with a risk of malicious compliance if pushed too far. That's an Ally with a base cost of  (for its power level), a ×4 modifier for being always available, and a ×1/5 modifier for Favour (meaning the ally will only help once ever), a +100% enhancement (Summonable) and a -50% limitation (Unwilling) will cost:
( 5 base × 4 freq × (1/5 favour) ) × ( 100% base + 100% enh - 50% lim ) =
4×1½ = 6.