There are several things going on here:


j.equalsIgnoreCase("a,e,i,o,u") will check if j (a length 1 string) is the string "a,e,i,o,u", which is almost certainly not what you want (since it's always false and therefore you set y=true for every consonant). Instead, consider setting a boolean value to false at the beginning of each iteration and setting it to true in the vowel branches. Then, if that variable is true, you know that this time you saw a vowel. Or just have the else branch.
You initialize y to false outside the loop, but once y is true it never gets reset, and so for each letter you will run the if (y == true) block.
Right now, your system only accounts for words with 1 y and no vowels. If you enter "yyy", you'll get 1 vowel &amp; 2 consonants.


Stylistically, there are a lot of other changes you can make to make your program easier to read through and debug. Here are a few:

You don't have to do "== true" when checking a bool. For example, instead of "if (y == true)" just do "if (y)".

All the vowels are handled the same, so you don't need separate branches for each. For example, you could have:

if (j.equalsIgnoreCase("a") 
    || j.equalsIgnoreCase("e")
    || j.equalsIgnoreCase("i")
    || ...)
{
    vowels++;
}


In fact, you can simplify this further by checking against a collection of vowel values, using a regex, or in this case, simply using contains:

boolean isAVowel = "aeiou".contains(j.toLowerCase());


Consider counting y's separately, so you keep track of vowels, ys, and constants in 3 separate counters. Then, at the end you can decide whether to add ys to vowels or consonants.

Finally, add a System.out.println("vowels = " + vowels + ", consonants = " + consonants + "...") to the inside of your loop during the debugging stage. This will make it a lot easier to see what is going on and where things start to go wrong.

Counting vowels with consonants
I will be a visiting scholar at a US university for 3 months. I have to leave the country twice to speak at conferences. I will not be returning home;only attending these conferences and returning to complete my visiting scholar stint.

Does such time out of the country: 
a) get deducted from the 90 day limit under the visa waiver program, 
b) make no difference and is the visit is seen as one continuous stretch of 90 days from initial arrival, or
c) "reset" the clock so that re-entry after my first conference starts a new 90 day period? (each conference related trip is about 7-10 days as the locations are very far away)  

As I will be out for 20 days, it's a big enough chuck of my stint that I'd like to "hold on" to it and not have it eat into my 90 days.
