After yesterday's frustrations, I may have found the cause of the problems I'm getting.
When you edit a toolpath in Fusion360, there are spaces to input your settings. Like stepover, feed rate, etc. An interesting feature Fusion360 has is that you can input equations, or in this case, they call it 'expressions' instead of a hard number. For example, say you wanted to have your endmill take 0.02" stepdowns, you would input 0.02". However, if you wanted it to take a percentage of your tool diameter, say 20% of a 1" tool, you would input "tool_diameter*.2," and the expression would change with the tool. This means if you decide to switch to a 1/2" endmill, then the expression now changes from 0.2" to 0.1" (0.5 * 0.2 = 0.1).
The thing is, when you have these expressions, there is virtually no way of telling when they change unless you look directly at them. This is where I think my problems are arising from.
When I input a value in one category, another parameter gets changed without my noticing, and I have no way of finding that out unless I either simulate every micro change or wait until after the part is made (which is too late). The solution to this problem is to remove all expressions and manually input the values myself.