This isn't too bad. I see four problems, though:
First, the index tokE and and counter count1 are updated whether or not there was an error. Depending on what they are intended to represent, you may want to update them only if a token was parsed successfully. By the way, why do you need both of these? Wouldn't one suffice?
Second, the use of member variables in inappropriate. Everything shouldn't be a member variable -- only those things that represent the state of the object, or at least only those that really need their values shared between methods. In this code, everything is a member, when many of the variables could and should be local. Using local variables would make understanding and debugging the code easier, because it's easier to be sure of what's happening while looking at only a small section of code at once.
Third, perhaps the biggest problem, is that the error message in the JOptionPane will report not the token that caused the error, but the following one, which will then be skipped. This is because in both the try and the catch, you ask the tokenizer for another token, but you really want both these blocks to be referring to the same token. Store the token in a
String variable (use a local!) then enter the try block and try to parse that variable. In the catch block, refer to the variable, not to the tokenizer. Now you'll get appropriate error reports and no more skipped tokens.
And finally, the size of the array tokenizedEntry is set before the tokenizer is even created, so you don't know how many tokens will need to be stored. You may be getting ArrayIndexOutOfBoundsExceptions if there are too many tokens to fit in the array. You could use the countTokens() method of the tokenizer to set the size of the array if you delay creating the array object until after the tokenizer is constructed.