int x = 0;
int Myarray[x];
int copied[x];
char holder[128] = {0};
while(derp.isnumber(holder) == true)
{
cin.getline(holder,256);
if(derp.isnumber(holder))
{
int c = atoi(holder);
Myarray[x] = c;
x = x + 1;
Arrays have fixed size. They don't expand when you access an out of bound element.
I didn't bother downloading your zip file. If you can't reduce it to some compileable version that can be posted here, you're not going to get get many people looking at it.
But, just looking at the snippet ne555 posted, you have code that is not legal C++ and 3 potential accesses to memory that you don't own (of which at least 2 are realized.)
There are no variable length arrays in C++ so lines 2 and 3 are illegal. (You're probably taking advantage of a compiler extension to enable them.)
If they were legal, Myarray and copied would never be capable of holding any elements, since you conveniently told the compiler they have none. Thus accessing elements of those arrays means you're accessing memory that you can't legally access.
holder is capable of storing 128 chars. You told cin.getline() it's capable of holding 256 chars, which also means you're telling cin it's okay to trample on memory you don't own and it certainly is not.