For finding out which PictureBox is pressed, your catWindow Sub should look like this:
Public Sub catWindow(ByVal sender As Object, ByVal e As EventArgs)
Dim box As PictureBox = TryCast(sender, PictureBox)
If box Is Nothing Then Exit Sub
'Now "box" refers to the PictureBox that was pressed
'...
End Sub
If you want to find it's location in the populate list, you will need to iterate through the list until you find the matching box. You could also pre-empt a property on your PictureBox that isn't doing anything else and use it to store the index. Older forms tools used to have a .Tag property especially for this kind of thing. But really, the need to do this smells like a design flaw to me.
FWIW, I'd rewrite your original sample like this:
If IsLoaded <> "free" Then
flow_display.SuspendLayout()
flow_display.Controls.Clear()
For Each box As PictureBox In populate
.Where(Function(p) p.parentID = 2)
.Select(Function(p) New PictureBox() With {
.Size = New System.Drawing.Size(697, 50),
.ImageLocation pw_imgLink & p.imageID })
AddHandler box.Click, AddressOf catWindow
flow_display.Controls.Add(box)
Next box
flow_display.ResumeLayout()
IsLoaded = "free"
End If