diff --git a/python/openapi/src/com/jetbrains/python/PathShortener.kt b/python/openapi/src/com/jetbrains/python/PathShortener.kt
index 9b09c1567c3b..19fdda2a92a5 100644
--- a/python/openapi/src/com/jetbrains/python/PathShortener.kt
+++ b/python/openapi/src/com/jetbrains/python/PathShortener.kt
@@ -11,6 +11,7 @@ import com.intellij.platform.eel.provider.getEelDescriptor
 import com.jetbrains.python.PathShortener.Companion.create
 import org.jetbrains.annotations.ApiStatus
 import java.nio.file.Path
+import kotlin.io.path.pathString
 
 /**
  * Replaces homepath with tilda and some well-known Windows vars as well.
@@ -58,10 +59,13 @@ class PathShortener private constructor(private val map: List<Pair<EelPath, Stri
   }
 
   /**
-   * Convert [path] to user-readable string replacing home with tild and so on
+   * Convert [path] to user-readable string replacing home with tilda and so on
    */
   fun toString(path: Path): @NlsSafe String {
     val pathDescriptor = path.getEelDescriptor()
+    if (!path.isAbsolute) { // eelPath doesn't support relative paths
+      return path.pathString
+    }
     var result = path.asEelPath().toString()
     for ((key, replaceWith) in map) {
       assert(pathDescriptor == key.descriptor) { "path is on $pathDescriptor, replacer is on ${key.descriptor}" }
diff --git a/python/services/system-python/src/com/intellij/python/community/services/systemPython/systemPythonServiceImpl.kt b/python/services/system-python/src/com/intellij/python/community/services/systemPython/systemPythonServiceImpl.kt
index f15727af1b94..bf19d3cecf79 100644
--- a/python/services/system-python/src/com/intellij/python/community/services/systemPython/systemPythonServiceImpl.kt
+++ b/python/services/system-python/src/com/intellij/python/community/services/systemPython/systemPythonServiceImpl.kt
@@ -137,7 +137,10 @@ internal class SystemPythonServiceImpl(scope: CoroutineScope) : SystemPythonServ
 
         }.toSet()
       // Remove stale pythons from the cache
-      state.userProvidedPythons.removeAll(badPythons.map { it.pathString })
+      val newPaths = state.userProvidedPythons.distinct().toMutableList()
+      newPaths.removeAll(badPythons.map { it.pathString })
+      state.userProvidedPythons.clear()
+      state.userProvidedPythons.addAll(newPaths)
       logger.info("pythons refreshed")
       return@withContext result.sorted()
     }
diff --git a/python/services/system-python/tests/com/intellij/python/junit5Tests/env/systemPython/SystemPythonServiceShowCaseTest.kt b/python/services/system-python/tests/com/intellij/python/junit5Tests/env/systemPython/SystemPythonServiceShowCaseTest.kt
index bdb1080f3c17..41273ff07137 100644
--- a/python/services/system-python/tests/com/intellij/python/junit5Tests/env/systemPython/SystemPythonServiceShowCaseTest.kt
+++ b/python/services/system-python/tests/com/intellij/python/junit5Tests/env/systemPython/SystemPythonServiceShowCaseTest.kt
@@ -4,21 +4,18 @@ package com.intellij.python.junit5Tests.env.systemPython
 import com.intellij.openapi.Disposable
 import com.intellij.openapi.application.ApplicationManager
 import com.intellij.openapi.diagnostic.fileLogger
-import com.intellij.openapi.util.SystemInfo
 import com.intellij.platform.eel.EelApi
 import com.intellij.platform.eel.ExecuteProcessException
 import com.intellij.platform.eel.ThrowsChecked
 import com.intellij.platform.eel.provider.getEelDescriptor
 import com.intellij.platform.eel.provider.utils.readWholeText
 import com.intellij.platform.eel.spawnProcess
-import com.intellij.python.community.impl.venv.createVenv
 import com.intellij.python.community.services.systemPython.SystemPythonProvider
 import com.intellij.python.community.services.systemPython.SystemPythonService
 import com.intellij.python.community.services.systemPython.SystemPythonServiceImpl
 import com.intellij.python.junit5Tests.assertFail
 import com.intellij.python.junit5Tests.framework.env.PyEnvTestCase
 import com.intellij.python.junit5Tests.framework.env.PythonBinaryPath
-import com.intellij.python.junit5Tests.framework.winLockedFile.deleteCheckLocking
 import com.intellij.python.junit5Tests.randomBinary
 import com.intellij.testFramework.common.timeoutRunBlocking
 import com.intellij.testFramework.junit5.RegistryKey
@@ -29,18 +26,12 @@ import com.jetbrains.python.PythonBinary
 import com.jetbrains.python.Result
 import com.jetbrains.python.errorProcessing.MessageError
 import com.jetbrains.python.errorProcessing.PyResult
-import com.jetbrains.python.getOrThrow
 import com.jetbrains.python.sdk.flavors.PythonSdkFlavor
-import com.jetbrains.python.venvReader.VirtualEnvReader
 import kotlinx.coroutines.async
-import org.hamcrest.MatcherAssert.assertThat
-import org.hamcrest.Matchers.hasItem
-import org.hamcrest.Matchers.not
+import org.hamcrest.MatcherAssert
+import org.hamcrest.Matchers
 import org.junit.jupiter.api.Assertions
 import org.junit.jupiter.api.Test
-import org.junit.jupiter.api.io.TempDir
-import java.nio.file.Path
-import kotlin.io.path.deleteExisting
 import kotlin.io.path.pathString
 import kotlin.time.Duration.Companion.minutes
 
@@ -68,6 +59,17 @@ class SystemPythonServiceShowCaseTest {
     SystemPythonService().registerSystemPython(randomBinary).assertFail()
   }
 
+  @Test
+  fun testRegister(@PythonBinaryPath path: PythonBinary): Unit = timeoutRunBlocking(10.minutes) {
+    val sut = SystemPythonService()
+    repeat(10) {
+      sut.registerSystemPython(path).orThrow()
+    }
+    val pythons = sut.findSystemPythons(forceRefresh = true).map { it.pythonBinary }
+    MatcherAssert.assertThat("No registered python", pythons, Matchers.hasItem(path))
+    Assertions.assertEquals(pythons.distinct().size, pythons.size, "Duplicates found")
+  }
+
   @Test
   fun testRefresh(@TestDisposable disposable: Disposable): Unit = timeoutRunBlocking(10.minutes) {
     val provider = CountingTestProvider(Result.failure(MessageError("...")))