C (tcc), 174174 111 bytes
Saved 63 bytes thanks to manatwork
i,b;f(char*a,int l){for(i=0;i<l;i++){if(a[i]=='a'||a[i]=='e'||a[i]=='i'||a[i]=='o'||a[i]=='u'a[i]==97||a[i]=='e'||a[i]=='i'||a[i]=='o'||a[i]=='u'){b++;ifif(b%2==0b++%2)a[i]=a[i]a[i]-32;}}}main(){char a[]="aeiou";f(a,5);printf(a);return;=32;}
Unminified
i, b;
f(char* a, int l) {
for (i = 0; i < l; i++) {
if (a[i] == 'a'97 || a[i] == 'e' || a[i] == 'i' || a[i] == 'o' || a[i] == 'u') {
b++;
if (bb++ % 2 == 0)a[i] = a[i] - 32;
}
}
}
main() {
char a[]a[i] -= "aeiou";
f(a, 5);
printf(a);
return;32;
}