Nevermind the entities, JPA, and custom constraints. This issue can be seen using normal beans with built-in validators.
Working on getting you a test case. You'll have to bare with me, as I have to set this up from scratch (including my solution) on a new system.

This is an example of how we are calling the validator:

	private TestBean testBeanBuiltIn;
	private ValidatorFactory factory = Validation.buildDefaultValidatorFactory();
	
	private Validator validator = factory.getValidator();
	
	private static final int MAX_ITERATIONS = 1000000;

        ...

        Set<ConstraintViolation<TestBean>> constraintViolations = null;
	for(int i = 0; i < MAX_ITERATIONS; i++)
	{
		
		constraintViolations = validateBean(testBeanBuiltIn);
        }	
        ...

	private <T> Set<ConstraintViolation<T>> validateBean(
			T bean) {
		
		Set<ConstraintViolation<T>> constraintViolations = null;
		
               // Call validator
		constraintViolations = validator.validate(bean);
		
		return constraintViolations;
	}	

That one is interesting, why do you use reflection in your class-level constraint? I'd expect you could access the entity state via normal field/getter accesses?

The code above shown in the code above, our we have a method that can take any bean class, and have over 500 different bean types that can be passed.
I've attached an example bean using built-in validators.

TestBean.java