Java APIs

I recently had to format my PC after data corruption, and
whe I reinstalled the Java SDK I found that certain programs
would no longer run after compiling. The problems seems to
be something to do with the input/output. I've tried
reinstalling Java without any luck. The error is this:


Is the boat ready for the journey(y for yes, n for not)?java.io.IOException: The handle is invalid
at java.io.FileInputStream.readBytes(Native Method)
at java.io.FileInputStream.read(FileInputStream.java:192)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:183)
at java.io.BufferedInputStream.read(BufferedInputStream.java:201)
at Boat.performCheck(Ships.java:69)
at Ships.main(Ships.java:19)
Exception in thread "main" Exit code: 1
There were errors


And the code that seems to be affected:

void performCheck() throws IOException
{
char check;
System.out.print("Is the boat ready for the journey(y for yes, n for not)?");
check = (char)System.in.read();
System.in.skip(2);
if(check == 'y')
{
seaWorthy = true;
} // close if block
else
{
seaWorthy = false;
} // close else block
} // close performCheck method


I'm learning Java through a course with a deadline of
November, and this problem is really slowing me down.
Can anyone help? The code compiles without errors, it
just won't run.